pokeshifters-shadows reborn
by conmanay
Summary: Cipher had returned, with a plan more sinister than anything ever seen before. Now a group of young heroes must brave the darkness to stop cipher once and for all.
1. Chapter 1

Chapter 1

Alex's POV

"And that's a rap" I said as I dashed out of school. I was about to the doors; I might get out in time I thought. "Hey freak" I shuddered at the sound of this voice, my local bully Chris and his friends had found me again. He has been on my case since grade school, why you ask? Short answer: I'm different, long answer: I'm a shifter. Shifters are humans that are born with the ability to turn into a Pokémon, in my case a Lucario. It is a hereditary trait in my family, but most of the time it's a random gene. 1/1000 is the normal odds of someone having the gene, but if someone in your family tree has it the odds go up. My mom is also a Lucario shifter, but she tends to hide that. Honestly it's not that bad if no one knows. However, I barley ever spend time in my shift from, due to the fact that shifting excludes clothing. Every time I shift I have to rip my shorts and poke a hole in my shirt; it's no fun so I have to wear shorts with elastic all the time. "So freak what are you gonna do today, huh" he taunted me. I sighed "dude just leave me alone" I said as I slammed my locker shut. "Or what" he laughed. I said nothing and headed out the school. I knew what he was doing; he was trying to get me to shift, which can happen if I lose my temper enough. I was just outside the school when I got thrown to the ground out of nowhere. I tried to get up but I got kicked in the side. "Come on freak, why don't you defend yourself huh. I could only curl up into a ball as I was beaten by his friends. Eventually the onslaught stopped, and then I heard Chris say" making it tough huh, well how about this he said as he grabbed my only pokeball out of my bag and opened it. My Eevee appeared and he grabbed it saying "I guess I'll try him next. That was it, I felt nothing but rage at that moment. I shifted in an instant. Just as he swung at my Eevee I lunged at him. I punched him in the face, knocking him to the ground and knocking out one of his teeth. As his friends ran off I readied an aura sphere in my hand fully intending to slam the ball of energy in his face. Luckily for him I came to my senses and stood up. I shifted back to normal and recalled my Eeeve just as the principal arrived on the scene. "What is going on here?" he demanded. Chris stood up and said "this freak attacked me" Principal Adams looked at me and said "you, office NOW" he yelled as Chris ran away balling.

"You beat up a student, he lost a tooth and has a broken nose" I sighed as my mother responded "the other student was attacking him and his Pokémon" the principal raised his hand silencing my Mom "maybe so but he is used his powers and severely injured a student and that is unacceptable, consider yourself expelled" my jaw dropped open. My Mom stood up and said "let's go home Alex" I nodded and stood up; there was nothing left to say.

As we drove home my mom said "I want you to know that you did nothing wrong" I sighed and said "I know, but what now" my mom just sighed. We drove the rest of the way in silence.

As we ate dinner we said nothing. Then I felt it, a presence. Lucario have some psychic abilities, not as much as an actual psychic type but I could tell when I was near a powerful psychic. "Do you feel that" I asked. My mom nodded "yea I feel it too". Then there was a knock at the door my mom walked to the door and opened it. There were two people in the doorway, the man was in a black suit and a red tie, his hair was black with just a few hints of grey. The boy behind him was my age he was wearing sunglasses at night for some reason, other than that he looked completely normal. The man was holding a black cane with a sliver handle. He had a gentle smile on his face, his aura seemed happy and calm. he finally broke the silence "hello my name is professor Andrew Malcom, may I come in". My mom seemed nervous "why" she asked timidly. He looked at me and said "I am the headmaster of a special school, and I'd like your son to enroll"…..


	2. Chapter 2

Chapter 2

Alex's POV

As the man and the other boy sat down in our living room my mother was still confused. "So why are you so interested in my son attending your school. The man

chuckled "well let's just say you and your son have a very special trait that i share with you". My mom frowned and said "how did you know that". He smiled and said

"every time a shifter is born the hospital makes a record of it". My mom still seemed cautious. "Prove it" i said quietly,"Alex" she scolded me. The professor raised his

hand "please, he needs to know that im sincere". He took off his jacket and rolled up his sleeve, his arm turned green and thinned, become razor sharp along the edge.

Where his arm once was there was the bladed arm of a gallade. He shifted it back and pulled up his sleeve. "Not only that but your son has one of the highest IQ

numbers ive seen in a long time" he continued. My mom seemed to relax a little "so professor Malcolm, tell me about your school" she said curiously. "Well you see im

am the headmaster of a school for gifted people, and while your son's grades are not the best i believe that is due to other students interfering with his work, am i

correct"? I nodded reluctantly. The professor then looked at me and said "while my school was originally for the intellectually gifted, i decided to begin a special wing of

the school with dorms for shifters to get an education without trouble from students who do not respect their differences". My mom looked at me, i nodded and smiled

"alright then where is this school". The professor nodded "its in Sinnoh, Veilstone city to be precise" he explained. My mother frowned and said "that's a long way from

here in Jhoto". The boy next to the professor said "the school pays for the travel arrangements". I looked at him and said "what's your name, and what's with the

glasses" ? he gave a small smile "Connor and im a gabite shifter, light is hard on my eyes so i just wear these. I nodded as my mom said "what do you think honey" ? I

smiled and said "when do i start" the professor stood up and pulled a ticket out of his pocket "perfect, you flight leaves in 3 days" he said as he handed my mom the

ticket. With that he and Connor stood up and headed for the door" as he walked out he said "see you soon". I smiled as i thought _this day is looking up after all_ ….


	3. Chapter 3

Chapter 3

Connor's POV

As me and the professor were driving away from the house, he was smiling "I like him, he's strong, smart reminds me of when i first met you in fact."

I frowned. "Well, I guess just another friend to hang out with."

The professor frowned and said, "We really need to work on your social skills".

I shifted in my seat at that comment, "Why, we already did that".

He frowned and looked me straight in the eyes. "You just sat next to me and just looked around, and with those glasses on you gave off a weird vibe," He said bluntly.

I pointed at him and said, "You know very well why i wear these. I hide my emotions and thoughts better than you do."

He sighed and said, "I won't argue that, but lucario's sense emotions in a slightly different way and while they probably didn't sense anything but they might in the future during training."

I put my hand on my forehead, "Well I'll hide from that detection too."

The professor pointed at me, "You can't hide forever, I'll run out of fake stories and exercises eventually." he said.

I threw up my hands and said, "Then what, you'll sell me out?"

He shook his head and said, "If anyone, and i mean anyone from a student to MRPA Director Michael asks, I'll say if you want to know why he disappears every now and then for a few hours,why he always wears pitch black sunglasses day and night I'll say ask him, because I can't tell you, that's what I'll say exactly like that." He then opened a a book and turned away. That was the end of that there was nothing more to be said.

? POV's

I looked at him dead in the eyes. "Maintain your cover at all costs, send updates via your new cell phone once a week, on a different day every time, do you understand Ethan?"

The brown haired, pointed eared boy nodded, and said, "Yes, Doctor Gregavich".


	4. Chapter 4

Chapter 4

Alex's POV

Chapter 4

Alex's POV

As I arrived at my classroom, I was on edge. The classes throughout the day had been with normal students, but this was the shifter only class. I was nervous, no, I was terrified. Who was the teacher? Would I like the other shifters? What would we be learning? As i sat down there were four other people there. One was a girl with black hair and green eyes wearing a black sweater with blue jeans, her most notable trait however was the yellow highlights in her hair. The other boy who seemed to be her brother was wearing a dark orange hoodie,his hair was charcoal black.

"Hey I'm Cassie, and this is Jake." I said nothing, "Shy much? Don't be!"She said in a jolly voice. I managed a smile.

Her brother interrupted her, "It's day one Cassie. Of course he's shy. Not everyone's a social butterfly like you." She quieted down at that remark.

With that, I took notice of the the other two students. One had brown hair and blue eyes with pale skin. His ears were slightly pointed at the top. He sat there with a silent expression on his face wearing a long sleeved purple button up shirt, black skinny jeans, and a pair of black tennis shoes. The other boy was wearing a red shirt and and brown cargo pants. He seemed like he had trouble sitting still. The silence in the room was finally broken when the door opened and the professor walked in.

"How are we today, class?" He asked with that same warm smile on his face. No one said anything. The professor nodded then spoke, "I see many of you are wondering the true nature of this class and I am here to dispel any rumors you may have." He said. "This class focuses on your shift abilities, how to use, control and counter other shift abilities." The entire class seemed to be even more nervous. The professor's smile faded slightly "However, I will not be your teacher. I must see to the entire school. Not just you five, and luckily, I have a very able teacher." Then another person entered the room. The professor stepped aside.

The boy turned to face the class. He looked at us and said, "I'll be teaching you. And while I may not look it, I have more experience than any of you." I was about to object when he put his hand on his glasses and finally took them off. As the dark glasses came off the entire room stared. Two red eyes, as in blood red with black pupils. "As you should know, experience outranks everything."

 **author's note**

 **i made an error but have corrected it. his eyes are red not golden.**

 **leave a review, i would appreciate it but you don't have to..**


	5. Chapter 5

Chapter 5

Charlie's POV

As we entered the gym we were waring new black jumpsuits that we were given. Our instructor was wearing one as well. "As you know shifting is a little hard on clothes, so me and the professor came up with these, these shift suits shrink or grow to fit the body their on". He said. We all had our doubts to say the least. "Don't believe me huh, well i evolved recently so i'll demonstrate" everyone stood back, if if evolved than that meant he would completely shred his clothes when he shifted. He pointed to a button on his jumpsuit wrist "press this and it calibrates the suit to your body, press it again, it deactivates and you can take it off". He pressed the button on his suit and it glowed blue around the edges. He then closed his eyes as his skin turned into blue scales, his arms turned into fins with a bladed claw on the front. He grew in size while sprouting a large tail and blue dorsal fin, the suit simply allowed the dorsal fin to pop out then reformed at its base . Finally his head changed into a blue snout with razor sharp teeth. In his place was a fully grown garchomp with a black suit around him. Everyone was awestruck, he gave a toothy smile then said "cool huh" .With that he closed his eyes and began to shrink, scales gave way to skin as his hands reformed, his head returned to a human one and his tail and fins disappeared. The suit reformed and covered holes where his fins and tail were. He opened his eyes fully human "see nothing to it, your turn" he remarked with a smug grin. We nodded and shifted one by one.

Soon there was a lucario, espeon ,houndoom and manectric alongside me. I shifted as well into a blaziken. He looked at us one by one then said "alright then, let's get to work"

Jake's POV

I was panting as he said "that will be enough for today" everyone breathed a sigh of relief and shifted back. He looked us over "i know you can do better that that" he said in a condescending tone. We were all too tired to object. He then headed for the door "same time tomorrow" he remarked as he left. We all simply headed to the locker room, that was pure torture to say the least.

Connor's POV

As i entered the professor's office he was reading a book at his desk. "How did the training go" he asked casually. I frowned and said "they have potential but that's about the only positive note" he looked at me and said "i see, well try to go easy on them". I looked at him dead in the eyes "easy won't get results only being tough will get results, that's how the real world works" he nodded "true but they need to learn the right lessons the easy way, can't you understand" i threw up my hands "ok i'll go a little easier" i exclaimed. He gave a smile "good, anything else" he asked sincerely. I turned around and walked towards the door "nah im going for a jog, see you at dinner" he sighed and said "ok be safe" i looked at him "don't treat me like a kid, im older than you". He nodded "yes, but for your kind your still a kid". I groaned and left the room...


	6. Chapter 6

Chapter 6

Jake's POV

"Again," Connor demanded. I was so tired of that command. It had been eight weeks since our training began, and it was only getting harder. After ten brutal exercises, he finally relented. "That will be enough for today." Everyone shifted back. "Alright, now that training's over, we have a special guest." Then a new man entered the room. He was wearing a brown suit with a green tie, he had emerald eyes and ginger hair.

"Hello everyone, my name is Michael, and I'm the director of the MRPA." Everyone looked confused. "The MRPA maintains security around the world, and we are starting a new shifter division."

We all frowned, "Wait, you want to recruit us?" I asked timidly. He nodded, "Yes, you see, shifters are not common knowledge to everyone, and while most people try to accept them, there are some who discriminate them or use then for malicious or even inhuman purposes. We need a response team to deal with the threat of shifters who do not wish to live peacefully." We all were caught off guard. "I need your help." We looked at each other, the head of the MRPA needed our help, and what was the point of all this training if we never used it?

The espeon shifter stepped forward, "I'll do it." We did the same. He gave a smile and said, "Great, I'll have an assignment for you soon. In the meantime, keep training." We all nodded and left.

3rd person POV

Michael entered the professor's office with a smile on his face.

The professor looked up and said, "So they all agreed? Good."

Michael nodded, "Yes, I think they'll be very helpful," He responded. The professor then looked out the window, "I take it there is something else you need to discuss with me," He said in a dreary tone.

Michael raised an eyebrow "How did you know that?" he asked calmly.

The professor gave a deep sigh, "You should have no other reason to visit me with how busy you are. You know you have my support on the shifter division, so what is it?" The professor asked bluntly.

"Well, it's time you're honest with me. What is your adoptive son's shift form?" He asked in a harsh tone.

The professor's smile disappeared and he turned around revealing an icy gaze. "What do you mean? He's a garchomp". He stated in a stone cold voice.

Michaels emerald eyes tightened, "Don't lie to me, Andrew. We looked into his file. All his info is fake." The professor's face was emotionless, "That is none of your business. Don't you have more important things to do than worry about my son's adoption papers?"

Michael clenched his fist "Your reaction alone proves your hiding something."

The professor's eyes went from calm to rage instantly "I can't tell you," he said, as he turned away from the director.

Michael banged his fist on the desk, "As the director of the MRPA I order you to tell me!"

The professor was silent for a while, then he turned around and spoke with authority, "If you want to know why he disappears for a few hours every night, or why he constantly wears pitch black sunglasses in public, ask him because I can't tell you."

Michael scowled at the professor then said, "Fine, I'll ask him, but if he doesn't talk either I'll bring you both in for interrogation on charges of falsifying official documents and conspiracy." He then turned around heading for the dorms...


	7. Chapter 7

onnor's POV

"That went well." I thought as the director left. I told him the truth, plain and simple. He understood and decided to keep my secret. That was that. I then opened a drawer in my dresser, retrieving a small metal necklace with a gem in the center. It more resembled a collar than a necklace however as it was for me in my true form. I sighed, hiding in plain sight was easy for me but it's lonely when only two people know the truth. I then focused on the collar, and it changed into a normal looking necklace. I decided I should wear it around my neck rather than keeping something so valuable in the dorms. I went outside and took off to get some exercise.

Ethan's POV

I entered the doctor's lab only to find him over a microscope . "Hey, Gregavich, I need to-." He raised his hand and quieted me.

"How many times have I told you? Do not disturb me when I'm working!"

I looked curiously at the vials on the table, "Are those the finished serums?" I asked him as he stood up and retrieved a vial full of purple liquid from the chemistry rack.

He held up the serum, "Behold my crowning achievement, the XY420 serum!"

I raised an eyebrow and said, "How do you know this one will work?" He looked at me with distain in his eyes "i had to cut open 3 subjects to get the necessary blood to finish this serum. And you know I don't waste assets."

I nodded, "Fair enough. So who is going to get the honor?".

He gave a wicked smile as he put the purple serum in the syringe, "Only one person is worthy of that honor. And that person is me!" He exclaimed as he injected himself with the serum.

He hunched over in pain, falling to his knees groaning in agony. I went wide eyed, "Doctor, you okay? Answer me!" I demanded.

He stood up with the same wicked smile on his face, "I'm fine. It worked. I feel so powerful!" He yelled to nobody in particular. He then looked at me, "Tell the master it worked. But if he wants more serums, I need more shifters." He said in a joyful tone.

I nodded and responded, "You may wanna practice with your powers. The master will want some proof." He smiled and raised his hand. His entire table and lab equipment began to levitate. I stepped back fearing something would go wrong, but he simply lowered his hand and the objects floated back to the ground.

He motioned for me to leave, "There's your proof. Now begone! I have much work to be done."


	8. Chapter 8

Chapter 8

Alex's POV

'This isn't scary at all.' I thought as we sweeped the warehouse. Despite no apparent danger, we were still on edge. It was our first major mission. After six months of butal training from Connor and tactical training from the MRPA, we were sweeping the warehouse for any contraband. I could literally feel the fear in the air, sensing emotions has it downsides. We were down to the last cargo carte when Ethan raised his fist.

"Hold," he whispered. We all stopped as he closed his eyes and focused. He opened his eyes. No explosives, but this case is different. He gingerly opened the crate and pulled out his prize form the box. It looked like a rocket launcher. Ethan looked it over and said, "It's not a rocket launcher. It's a M28 Electro Net Launcher developed by Silph Co." He explained.

Jake radioed fo the MRPA soldiers to come in. The crate was sealed and taken away. We got on the chopper and headed back to base.

Jake's POV

Michael debriefed us as soon as we entered the command center. "This is a major problem. If these fall into the wrong hands, a lot of innocent pokemon are in trouble."

I frowned and said, "What do you mean the wrong hands? You always are saying that, but you never tell us who."

Michael sighed and said, "I can't tell you that." He said turning to walk away.

I stood up and yelled, "We're risking our lives for you, and you won't tell us what we're up against!"

Michael sighed, "Fine, come with me." We all followed him to the elevator. We entered the door and michael turned to the elevator screen, "Sub level six," He ordered.

The computer spoke and said, "Six occupants do not have clearance to enter that area."

"Director, override Pierson, Michael." He responded. The elevator beeped and began to move. Michael turned to us, "This is classified info. Your eyes and the professor's only. Understood?" We all nodded as the door opened. As we left the elevator we were walking by holding cells. The occupants of the cells were unlike anything we've seen. They were pokemon but different. Their skin was a shadowy black, and their eyes were glowing blood red with no pupils. We were all on edge. Cassie looked terrified.

"Wa-what are they?" Charlie asked timidly.

Michael chuckled, "See why I don't share everything?" He asked bluntly. The only one who wasn't terrified was Ethan. In fact, he was smiling. Michael then took us to a window that looked down into a massive wall filled with holding cells. He pressed a button and a cell was taken from the wall and brought up to our level by a large mechanical arm. We were face to face with a pitch black absol. It was snarling at us through the glass.

Alex was staring at it, "All i senese is rage, mindless rage" he said in a shocked voice

Michael nodded and pressed a button on the console, a blinding flash filled the cage. When the light dissipated the absol was normal but was out cold.

Michael turned to us and began, "Twelve years ago, a group called Cipher created Shadow Pokémon, and used them as weapons. But they were wiped out, or so we thought." He then pressed a button and three scientists took the absol away. "Cipher is a tough nut to crack. Every time we crush them, they just go underground and reform." He explained. "The shadow pokémon we have here are the first of many that Cipher has created recently with what we call shadow energy. We believe they are working on using shadow energy to enhance shifters. These shadow pokémon are harder to purify then the originals. It takes a month to suck out the shadow energy enough to purify them. It's just not fast enough, but its all we can do." He said sadly. He then motioned us to follow as we headed back to the elevator.

"We need you to help us find and destroy Cipher's factory. Otherwise, they'll just make shadow pokémon faster than we can purify them." He told us as the elevator moved. We said nothing to him as he left.

We all arrived back at the school, and decided to pack our things. It was summer break after all. That definitely improved our moods. We all needed a good long rest.

Andrews POV

I was getting ready to leave when Connor entered my office. "Hey, Andrew" he said casually.

I gave him a smile and replied. "Hello, I was just getting ready to leave. The others are gone for summer. Will you be staying with me?"

He shook his head and said, " Nah, I'm gonna go visit my cousin in Altomare."

I nodded, and said, "Okay, enjoy your break." At that, he turned to leave. He was opening the door when I stopped him. "Please, be careful." I requested.

He laughed and said, "I'll be careful. Worry about yourself old man." He joked, then left.

Ethan's POV

I was dropped off in the city and slipped into a back alley. I pulled out my phone and called the number. I was answered with silence. I sighed, and said, "Access Code Four Sierra Delta."

There was static, then a voice came over the line. "Hello, Ethan. Did you get away unnoticed?"

"Yes, Doctor Gregavich. I told them my dad was picking me up, and they bought it." I responded.

He laughed, then said, "Good, they suspect nothing then. Warp to the extraction point, and I'll scramble a VTOL to pick you up."

I nodded, and said, "Yes, I'll be there soon, Doctor."

"Good, hail Cipher!" He exclaimed.

"Hail Cipher!" I responded as he hung up. I was then interrupted by a police officer approaching me.

Third person POV

The officer approached the boy cautiously. "I heard that entire phone call, buddy. Sorry, but you're under arrest". He said as he pulled out a pair of cuffs. Ethan held out his hand, and a sword materialized out of nowhere. The cop pulled his gun, but it was sliced in half by Ethan's sword before he could react. Ethan kicked him to the ground.

The officer was terrified as Ethan lifted his blade "Please, I have a family. Don't do this!" he begged.

Ethan's eyes were cold, as he said, "I'm sorry." In a fraction of a second he plunged his sword through the officer's heart. Ethan then closed his eyes and vanished in a white flash.

Authors note- DUN DUN DAAA! Yep, Ethan is evil.

Sorry for the long wait school has been kicking my ass.

As a side note, Ethan was not with the Doctor in chapter seven. That was a typo.

Leave a review if you want :)


	9. Chapter 9

Chapter 9

3rd person POV

The sun was high in the sky, it was pleasant and peaceful. The sound of the breeze flowing through Altomare's canals were soothing to the two people sitting on a bench near a park. One was tall with blond hair, stocky and wearing pitch black sunglasses. The other was tall but skinny with black hair and grey eyes. Despite the appearance of them having no relation to one another they were blood relatives. One of them was eating an ice cream cone and the other was drinking a soda.

"I don't know how humans stomach this stuff," Connor said bluntly.

Norin took a lick of his cone "It's not that bad, but I can see why some people don't like it." He responded. Norin stood up and Connor followed suit. Norin then looked around "Clear," He said in hushed tone. He then looked like he was about to dive into the canal when Connor grabbed his shoulder.

"Can we just walk? I haven't seen you in almost a year." Norin looked like someone had shot him. Connor Gave a sad smile, Norin nodded and followed Connor down an alley. As they were walking, Norin finished his ice cream cone, however there was no visible ice cream on his face. Connor shook his head, "I don't know why you like human food why not just magikarp, honestly i don't like human food and, I live with them."

Norin pointed at Connor, "Hey, I like fish, but when your main job is to fish for everyone you tend to like to mix it up from time to time." He joked.

Connor chuckled and said, "Ha ha, okay, isn't it just unusual for a current chaser not to like just fish."

Norin gave him a weird look, "And it's not weird for a sky dancer to live with humans when it's safer here." Norin jeered back.

Connor face palmed "Like I said, I prefer to just stay hidden, and nobody will look for me there." He explained. Norin gave a 'really' look and said, "That's a lie. You just don't trust anyone." Connor turned his face away.

Norin decided to change the subject. "Have you ever thought about you know...finding a mate."

Connor raised an eyebrow, "With my trust issues, you really think I can claim anyone?" He asked sarcastically.

Norin laughed, "Connor, you're a sky dancer who has above average abilities in every other trait. You could have anyone in the garden if you wanted them." He said bluntly.

Connor shook his head and said, "Maybe, now let's fly." With that, Connor disappeared in a flash of light, then there was a small woosh sound as a invisible entity took off at an incredible speed.

Norin humphed "Showoff," then he disappeared as well.

Jake's POV

"I win" Cassie exclaimed.

I sighed "you know you're pretty ruthless, when it comes to games" I said as we turned off the console.

Cassie shook her head "nah I'm just competitive" she said in a sarcastic voice.

I then turned on the news only to see a familiar face being interviewed , it was director Michael.

He was talking about the MRPA's investigation into Silph Co.

"you ever think we shouldn't have signed up for all this" I said thinking out loud.

Cassie looked at me with a frown "what do you mean" she asked casually.

"You know cipher, shadow Pokémon, secret weapons" I explained.

Cassie gave a small smile "that's why we do it, there's too much wrong in the world to do nothing, and if we just stand by and let it happen when we know we can help then how are we better than the bad guys" she said in a strangely serious voice.

I sighed and said "you're always the good one, I stay because you do".

She smiled and laughed "ah my big brother, always protecting me". With that she stood up "I'm gonna go help Mom with dinner" she said as she walked away leaving me to my thoughts.

 **Author's note-special thanks to Storylover Vodhr- Dux Ducis for letting me use some of his ideas in my story, check him out he's a way better writer than me.**

 **The next few chapters will be about the other main characters summer break, don't worry there will some action in them but it will mainly be character development**.

 **As always please leave a review, i love the feedback.**


	10. Chapter 10

Chapter 10

3rd person POV

Doctor Gregavich was once again completely absorbed in his work. He was known to lock the door to his lab for days when he believed he was on the verge of something great. As he was finishing the shift collar he mused on his new powers. He was more than proficient with telekinesis and multiple defensive techniques. His greatest skill however was his more psyche related abilities, mind reading and teleportation. Even mental control! Such abilities were astounding to the new shifter. He could defeat any opponent with a mere flick of his wrist. He sautered the last wire and closed the panel, then he sensed someone behind him.

"Ethan, how many times have I told you not to-." He turned around and was met with a familiar pair of amber eyes.

He instantly was quiet in her presence. "Hello, Doctor. It's been a while." Said the woman in an irritated voice.

She was wearing a black woman power suit with a Cipher logo on the breast pocket, with long black pants to match. Her hair was an unnaturally dark red.

Gregavich bowed slightly and said "Prefect, Lana. To what do I owe the pleasure of this visit."

She scowled at the doctor. "I believe you already know why I'm here doctor. You haven't been giving updates recently." She said in the same harsh voice Gregavich had learned to despise.

She looked at his workspace, "Must you be so untidy? Well, where is your progress report?" She demanded.

The doctor quickly rushed over to another table and handed her a data pad. "That is all the data on my recent findings that the master requested." He stated timidly.

Lana skimmed through the data pad then turned it off. She turned her head and began to walk away, her high heels clicking on the floor.

She opened the door and said, "You have one month to give the master some real results, or there will be consequences!" She then slammed the door behind her.

Gregavich groaned and went back to work. Why that woman was the master's second in command was beyond him. She was arrogant, snide and condescending. One day he would take her down a peg but for now he had to work. One does not disappoint the master.

Lana's POV  
As I was leaving. I noticed a grunt being dragged away to a cell.

"What did this man do?" I demanded.

One grunt turned to me and said, "He tried to steal a flash drive. He's an MRPA spy."

I nodded and said, "Put him on his knees." The soldiers kicked him to the ground. I grabbed the man's face and kneeled to be face to face with him.

"No one betrays Cipher and lives!" I said coldly.

A powerful burst of electricity surged through my hand. The man screamed as the electricity pulsed through him. The man passed out and I let go of the spy. His body fell to the ground, singed and unmoving.

I then smiled at the two soldiers. "Well done you two. You may return to your stations."

"Yes ma'am!" They yelled in unison. They then dragged the spy's body away. I chuckled and continued towards the helipad. The master was waiting for my return, and one is not late for such a meeting.

Charlie's POV  
I was greeted by the smashing of glass when I came home, my dad was drunk again. My mom had run off when I was eight. My dad was always gone. Gambling, shady jobs, you name it. For those reasons. I had learned to fend for myself by the time I was ten. Being a shifter was a blessing in all honesty. It was a lot easier to intimidate people into backing off when you could make fire out of nothing. I only used my powers for self-defense. Nothing more. I was determined not to become my dad. I simply decided to go to my room. It was best to just leave my dad be. However he had other plans. The smell of alcohol was thick around him.

"Hey, I need your help." He said in a slurred voice.

I simply ignored him. He always kept trying to get me to help him with his "business ventures". "Get out!" I yelled.

He shook his head. "Fine, you're just like your worthless mother." He mumbled as he left.

Something was off. My dad never gave up that quickly. Against my better judgement, I decided to look around. He had told me when I arrived to stay out of the basement. He was gone already. Probably to restock his liquor cabinet. I creeped down the stairs and looked around. I could hardly believe what I saw. The room was packed with large tubes filled with a black sludge that appeared to be emitting smoke. Was this the shadow energy Michael told us about?

"Pretty, ain't it?" My dad said behind me.

I turned to him. "Why are you storing this stuff?!" I demanded.

My dad smiled "I'm making a fortune on it. I store it before it's transported, then I get paid. Simple as that" he explained.

"Dad, this stuff in dangerous. This goes beyond alcohol and drugs. They could lock you away for life if they bust you!" I yelled.

My dad waved his hand. "Meh, the thing is they won't catch me!" He said confidently.

I scowled at him. "I'll turn you in then!" I yelled even louder. His bloodshot eyes went wide, as if he sobered up at once.

He reached into his pocket slowly. "Sorry, Charlie." He said, with genuine sadness in his voice.

He pulled a gun, but I was more than ready. I dodged the bullet and grabbed my dad's gun, heating up my hand. As I did so, the gun melted in my dad's hand. I punched him in the face and knocked him out cold. I sighed and pulled out my cell phone. It's time to end this.

Soon the MRPA arrived and took my dad away. I simply sat down in the MRPA's truck and waited. This is going to be a long night.  
 **  
Author's Note- Hint, Lana will be very important later on. So keep an eye on her. She is not someone to be messed with.  
Please leave a review. I want feedback.**


	11. Chapter 11

Chapter 11

3rd person POV

Summer was over. It was the first day of class, lunch to be specific. Alex was chewing on his sandwich, however food was not his main concern. He looked across the lunchroom and saw Cassie and Jake eating with some other people. Jake was transfixed on cassie, deep in thoughts. He liked her, no doubt about that but he had no idea how to tell her. He couldn't seek advice from anyone in the group, Cassie would find out. He simply needed to think of the right move.

Charlie's POV

I was eating lunch away from everyone else, after what happened over summer i just wanted to be alone. "Tough summer huh" someone said behind me. I turned around expecting to see the professor, but it was Connor. "Leave me alone" i mumbled as he sat down next to me.

Connor chuckled and said " i know exactly how you feel" i turned and frowned "no you don't" i said defiantly. Connor shook his head "yes i do, you feel sad and betrayed, someone who, despite their faults you genuinely cared about tried to kill you, and now you have no family left" he said in a calm voice.

I was awestruck, "you're not a psychic how did you know that" i demanded.

"I trained all of you, i can tell when any of you guys are off, that and the professor filled me in" he admitted. I said nothing. "Believe me, i know family issues, but in the end it's your choice. You can either be sad and give up on life, or you can keep fighting and amount to something, the choice is yours" he said in a kind voice. With that he stood up and left, there was nothing more to say.

Alex's POV

We were walking back to the dorms in the dead of night, connor ran us harder than usual today and we were all exhausted. Suddenly a chill went down my spine, i turned around only to see 4 people approaching us. "Who are you" i asked timidly as the others turned around.

The 4 figures said nothing, we all tensed back. Then the four men reached for their belts, "scatter" i yelled. As i said this the four assassins pulled out guns and opened fire, me and charlie dodged but the others were too slow.

Jake, Cassie and Ethan fell to the ground with darts in their necks. Then a bright beam of light blinded me, a aircraft with two tilted jet engines was overhead. "The doc said be fast, forget those two, we need to go" one of them yelled as i heard sirens in the distance. They threw Cassie,Jake and Ethan over their shoulders and boarded the jet. I stood there in shock, too stunned to do anything. The jet took off, disappearing into the cloudy night.

* * *

We were took to MRPA HQ immediately. We entered command only to see michael and the professor looking at a map.

"How did this happen" the professor demanded.

Michael shook his head "stealth jet, never saw it coming".

I walked up to the table "do we know where we went" i asked quietly.

Michael was about to speak but another voice interrupted him "yes we do" connor said as he entered the room. Everyone looked at him, "i tagged cassie's phone, it's near Tohjo falls".

Michael wasn't convinced "how do you know, they could of just threw the phone out" he said in a grim voice.

"they did, but i managed to find their trail, the cell phone kept pinging until Tohjo falls. I plotted the course from there, and i got a general area where they have to be otherwise nearby towns would have noticed them by now " connor explained.

Michael nodded and said "ok i'll dispatch a drone" he said as he ran out of the room. Connor then turned to me. "You said they were wearing masks, did they say anything" connor asked.

I shook my head and responded "i heard something about a doctor but that's it" connor's eyes went wide. He then turned and left saying nothing else.

I was about to go after him when the professor grabbed my shoulder 'he needs some time alone".

"Why " i demanded.

The professor frowned "he knows the doctor in question, just give him some time" he explained. I nodded, deciding not to push it. There were much bigger things to worry about right now…

Cassie's POV

I awoke in a large cell, the floor was cold metal. I got up slowly, still groggy from the tranquilizer.

"Ah you're awake, good" a voice said from nowhere.

"Where am i, who are you" i demanded.

The voice laughed "i am cipher's head scientist, but you may call me master" he said in a harsh tone.i noticed a mirror in the wall.

"Don't worry cassie, just comply" a familiar voice said. "Ethan, what, why are you". The doctor came over the speaker again

"your friend has been feeding me intel, he was working for me from the start" he explained in a snide voice.

Then a small metal arm emerged from a panel in the wall. The arm was holding a syringe filled with yellow liquid , i tried to shift, so i could zap the arm, but my body didn't shift, it just didn't respond.

"I'm afraid you won't be doing any shifting" he chuckled as i felt the syringe go into my arm.

Instantly my skin began to burn. I screamed in pain, falling to my knees. My face felt itchy, i then noticed my reflection in the mirror, my face was turning white. I felt my body growing, my bones cracking and reshaping. I then fell on all fours, yellow fur sprouting all over my growing body, my clothes were ripped to shreds as my body finished growing. I felt a pain in my jaw as two long razor sharp fangs extended out of my mouth. I let out a beastly roar as my transformation finished The pain subsided and i looked into the mirror. i was a large 4 legged yellow pokemon with a purple mane, i felt more electricity than ever before in my body.

"Incredible, it worked, a real living raikou" the doctor exclaimed. I then turned to the mirror. I didn't care who was in that room, they were going to pay. I let loose as much electricity as i could muster. However my attack was simply sucked into the roof like it was nothing.

"Feisty i like that" the doctor stated in the same snide voice.

He laughed once more and said "sweet dreams". I heard a hiss as a green gas poured into the room. I became drowsy and passed out, the last thing i thought of was "where are you jake" as my mind shut down.

* * *

Confidentiality Note: The information contained in this email and any attached file(s) are for the exclusive use of the addressee and may contain confidential, privileged and non-disclosable information. If the recipient of this email is not the addressee, such recipient is strictly prohibited from reading, photocopying, distributing or otherwise using this email or its contents in any way.


	12. Chapter 12

Chapter 12

Charlie's POV

"This looks fun" i joked as we looked over the factory.

It was huge, walls were tall as some buildings in veilstone, with multiple guard towers and missile defences inside the walls to deter air assault. The only way in was a massive iron gate and a helipad.

Michael shook his head "we don't have the means for a frontal assault, but i have an idea" he explained.

"Well what is it" Alex demanded.

"We need to create a diversion at the main gate, while a strike team insets here at the roof" he pointed to a maintenance door.

Andrew interrupted "how do we create a distraction big enough to occupy both the ground and air defenses so a team can get inside unnoticed".

Michael smiled "i have a friend who can help, he'll be more than enough to keep cipher occupied" he said confidently.

Connor was off to the side of the room "i agree with michael, he's got this" he said quietly.

Michael nodded and said "ok then, i'll be calling in all available agents, it will take two days to mobilize our forces at least".

Alex was about to interrupt but Michael stopped him "it takes time to mount an assault like this Alex, we get one shot at this" his voice was stern.

Alex sighed but nodded.

I then turned to Connor "your coming with us on this one right" i asked. Connor shook his head and left.

"Hey" i yelled as i ran after him.

* * *

I caught up to him in the hall and yelled. "What are you doing, this is cipher's main factory, cassie jake and ethan are being held prisoner, everything is at stake here" i said in a loud voice.

Connor didn't even acknowledge me.

"Answer me" i demanded. Connor stopped but said nothing. "Are you too much of a coward to help us" i yelled.

Connor turned around slowly. "You have no idea what i've endured, i can't be there" he said with hate in his eyes. He then walked away ignoring me all together.

"Fine, stand by and do nothing" i yelled as he turned the corner. I then left for command, i had more important things to do right now than worrying about him.

Connor's POV

I sat down in a break room alone, he had no right to call me a coward. I pulled out my necklace and looked at the stone in the center. I sighed "Dad, you always knew

what to say, but what do i do". I shook my head. The doctor had taken everything from me, he needed to die. However if i did go cipher would know i was alive, kill the

doctor and expose myself, or hide and risk them failing. Neither option was appealing to me. For the first time in years, i was uncertain of what to do….

* * *

Cassie's POV

I awoke in shackles, even with the strength of my new body i was helpless.

Then a voice appeared in my thoughts. "Cassie are you there" said a familiar voice. "Jake, where are you" i yelled out loud.

"I'm in a cell, some scientist injected me with something, im an...entei". Jake said in a sad voice.

"How am i hearing you, we aren't in the same cell" i asked.

"I guess these bodies come with telepathy" he guessed.

However before i could respond the door to my cell opened and a man entered the room. He was tall, wearing a white lab coat with a keycard on his belt and a large golden C with a purple outline on his breast pocket. His hair was black with the slightest hints of grey. He was wearing black chemical gloves and rubber boots.

"Hello my dear, how are your" he said in a casual voice.

"I'm going to tear you to shreds" i yelled with a beastly roar.

He laughed "really and how will you do that with your legs bound and my lightning rod diverting your electricity" he said with a vile grin on his face.

"How do you understand me" i demanded.

He chuckled and said "you know your kind has always fascinated me, the things you can do, the ability to change form, the powers you possess, i've always admired shifters, so i decided to take that power for myself".

"How did you do that" i asked in cold voice.

"Discovery requires experimentation, and i experimented with shifter blood to make a serum, the same one i used on you and your brother" He said proudly.

He then came closer and began to rub my cheek like i was his treasured pet. My neck was pinned to the ground, otherwise i would have tore his hand off with my new fangs.

He then stepped back and held out his hand, i instantly felt a pressure in my skull. "Now then, where is the MRPA's base" he said in a stern voice.

"I'll never tell you" i said as the pressure intensified.

"Comply, and your suffering will end my dear girl, i see your past, being abandoned by your mother, your big brother taking care of you till you were adopted out of pity. Being tormented at school, not being able to fight back" he said as he continued to pull on my mind. "

Get out of my head" i yelled. He lowered his hand and my headache stopped.

"Fine" he yelled as he came closer and looked me dead in the eyes. "If you do not comply there will be pain, more pain than you can possibly imagine, i will make you beg for death, but you will not receive it, I WILL BREAK YOU" he said in a sadistic voice. He then turned and left.

I felt like crying but i wouldn't give him the satisfaction. I simply closed my eyes and went back to sleep….

Gregavich's POV

I was heading back to my lab when my phone rang. "This is Gregavich" i said in the calmest voice i could muster.

A familiar voice came over the line, it was cold and sharp "Hello doctor i received your report, well done" said the master.

"Thank you master Ardos, i could not have achieved this without your support" i responded as calmly as i could.

"As for the subjects in question i hear you are having trouble with compliance" he said with disdain in his voice.

"Well i wouldn't go that far to say" i was interrupted by the master before i could say more.

"I am sending Lana to oversee your work from now on, she should arrive before nightfall,if you cannot break them she will". I was about to object but he hung up. Now i had to deal with Lana constantly. This day was just getting worse and worse...

 **author's note- please leave a review, it makes my day when there's a new review, even if its negative**

 **on a rather sad note my beta reader Mega espeon cannot continue due to his busy schedule, but i do not hold that against him.**

 **if anyone is interested in replacing him PM me.**

 **i have another chapter almost ready, if i get just 1 review i will post it then, otherwise it will come on thursday.**

* * *

Confidentiality Note: The information contained in this email and any attached file(s) are for the exclusive use of the addressee and may contain confidential, privileged and non-disclosable information. If the recipient of this email is not the addressee, such recipient is strictly prohibited from reading, photocopying, distributing or otherwise using this email or its contents in any way.


	13. Chapter 13

Alex's POV

As the rotors spun up the pit in my stomach only grew larger. The plan was straight forward enough, Frontal assault while me, connor,charlie and a strike team

infiltrated via skydive and shutdown the air defenses. Once we landed we would be on our own. Then it was time to rescue Jake Cassie and Ethan, ever since they were

kidnapped i kept telling myself they were fine but I just had a nasty feeling that we may be too late to save them.

I shook my head and dismissed it, this was not the time for hesitation. "10 minutes to drop point" the pilot said. I stood up as the strike team Connor,and Charlie put on

the MRPA's newest toy. Delta V glide wings. Carbon fiber wings with small thrusters and control arms like hang gliders, top of the line tech. The helmets had a HUD that

showed altitude and recommended flight path.

We put on our helmets and wings, then I stepped up to the back door of the VTOL.

"Alright we have our orders, shutdown the air defenses, rescue our people and execute kill/capture order on Doctor Gregavich". Connor shook his head and said " i vote

kill, he isn't some you take alive". Connor had told us a little about this doctor, and i couldn't say i disagreed, but he definitely knew too much information to just kill. I

just hoped michael's ground assault and his big diversionwould work.

* * *

Cassie's POV

I was woken by the door to my cell opening again, my blood went cold when i saw my visitor. A woman in a black suit was holding someone with a bag over her head at

knifepoint. "Playtime is over, tell us where the MRPA's base is or she dies" she said as the bag came off. It was my mom. My eyes went wide. "Wha please she has

nothing to do with this" i begged. The woman smiled "that's the point, is the MRPA really worth letting her die" she asked in a sad voice. "Please cassie listen to her" my

mom begged. "You have five seconds" the woman explained. I didn't find the words in time. She began to stab my mom right in front of me, over and over again. She

laughed at the top of here lungs as my mother's eyes went blank and her breathing stopped. "no , no please stop, stop" i wailed as hot tears streamed down my snout.

She then let go of my mom and her body fell to the ground, cold and unmoving, she didn't even seem bothered about the blood on her suit.

"You made the wrong choice" she chuckled in a snide voice.

My mind shut down, as if something else was taking control, the last thing I remembered was a feeling of pure hatred.

* * *

Gregavich's POV

As i was watching lana's little show i was genuinely impressed. Her illusions must be impressive to fool that girl. Suddenly the raikou's wailing stopped. "Doctor

brainwave activity is spiking drastically" one of my aids yelled. I looked at the readings, aggression was through the roof, and electrical surge was growing. "Lana, get

out of there" i yelled over the intercom. Just as i said this you could hear the crackling, the hair on my arms stood up, even outside the cell you could feel the

electricity in the air. With a beastly roar the raikou unleashed a blast electricity more powerful than i had ever seen, the lightning rod shattered and lana was zapped

point blank. She fell to her knees breathing heavily, her body smoking. She was hurt no doubt but her clothes and face were not visibly affected at all. She opened the

cell and left as the raikou continued to roar and tug on the shackles. This was not the girl we had been dealing with, this was a mindless beast. Lana walked into the

room with a glare pointed straight at me. "That lightning rod held up against Greevil's Zapdos, HOW DID SHE OVERLOAD IT" lana yelled at the top of her lungs."I don't

know, ive never seen an electrical attack that powerful, how are you still alive" i demanded. Lana was about to respond when a voice came over the intercom. "Doctor

we're under attack, the MRPA has a LUGIA, i repeat A LUGIA" The soldier yelled as a tremor shook the entire room. "Send out all available shadow pokemon, and

activate air defenses" Lana ordered. She then turned to the 6 Bisharps who acted as her security detail. "Stay here and protect the doctor, you two with me" she said as

they left the room and ran towards the command center. I looked at the BIsharps and said "i need to secure my lab follow me. The two steel knights nodded and

followed me as i sprinted towards my lab. As I was running towards my lab my mind was racing. How did they find us, is this lugia XD001, if so was HE here. I shook

the thoughts from my mind, there were more important things at hand then speculation about this attack, to be specific stopping this attack.

* * *

Jake's POV

I woke to alarms going off all around me. Maybe the MRPA had found us, but I didn't get my hopes up. Hope, that was a funny word. It had been a month, maybe more

since that doctor had started this nightmare. Time seemed irrelevant in this place, there was no real time, just a routine. Pain then food and water, rinse and repeat.

How could that man be so evil, he enjoyed bringing pain, hurting people, he didn't care for anything other than his "research". My thoughts were interrupted by a

tremor, like an earthquake. "Cassie, do you feel that" I thought. There was no response, were they stopping our telepathy? I reached out again,trying to connect to my

sister's mind. I found her, but I instantly wished I hadn't. My sister wasn't there, I could feel her but she mentally wasn't there. All I felt was rage,rage and sorrow. She

was just gone, her mind was nothing but feral anger . My eyes began to water, I couldn't hold the tears anymore, she was gone and I couldn't help her. I simply

collapsed and began to weep. My only thought was "I've failed you dad".

* * *

Alex's POV

"Go go go" I yelled as we jumped off the ramp. The descent was surreal. Even with the helmet I could feel the air rushing by me. Adrenaline was pumping through my whole body as we punched through the clouds

9,000 feet, my helmet beeped

"Now" I ordered over the radio

We pressed the buttons on our control arms and our wings deployed. The wings folded out and the thrusters kicked in. Our speed increased exponentially as the factory grew larger before us.

5,000 feet, my helmet reminded me.

"Wait" i ordered. We needed to wait as long as we could to avoid detection.

1000 feet - my helmet beeped even louder

"Wait" i repeated

800 feet, my helmet blared

"Level out, deploy shoots" i yelled over the radio

Our shoots deployed instantly, my body was instantly yanked back as my airspeed vanished. we floated down to the roof unnoticed. The others landed with no problem.

Me, Connor and Charlie shed out flight suits for our shift suits as the soldiers readied their rifles. "Remember, stealth" i whispered as we opened the door. We were in,

and there was no turning back.

 **Author's note**

 **Fans of my second favorite call of duty game will know where i got the inspiration for the skydiving scene. T** **his story will be sort of a spy/military story from now on, just fyi. don't worry pokemon will still be a main part of it**

 **Michael is the kid you play as in XD gale of darkness. That's why he has a lugia.**

 **Lana isn't just another shifter obviously, more on her later**

 **Tomorrow april 26 is my birthday. if you guys could leave a review about this story that would be like an extra present for me.**

 **Please leave a review, i would love hear your positive (or negative) thoughts on my story.**


	14. Chapter 14

Chapter 14

3rd person POV

"This can't be happening" the doctor said as a shadow Rhydon disappeared into a snag ball. The MRPA was snagging the shadow pokemon left and right, months of work

was disappearing before his eyes.

"Seems your pets aren't all you said they'd be" Lana scoffed.

"How was i supposed to know they had master balls" he jarred back.

A massive tremor shook the entire command center. he looked to the cams, only to immediately regret this decision. The lugia had blown open the walls, and there was

no patching the leak. Before i could say anything, the tower on the other side of the facility exploded. Lana shook her head then walked to a console and typed in a

number the doctor made sure was at the bottom of the list.

"Doctor what do you have to say for yourself" the master's voice ringed to the room.

Gregavich turned slowly to the monitor, his eyes full of fear "Master they breached the wall while simultaneously destroying my air defenses". The master's face was stone "i am aware, an impressive amount of coordination though not unexpected".

"What are my orders" Gregavich pleaded.

The master paused, the entire room was silent despite the explosions and gunfire in the background. "Doctor, return to your lab and gather what you need to continue your work. Lana, after the doctor has gathered his research wipe the servers clean and prepare the assets for transport".

The doctor was about to object but he stopped himself, He nodded and closed his eyes vanishing in a purple flash.

Lana turned to the master "i don't have a way to transport the assets" Lana said as calmly as she could. "I am aware of that as well, i already have a stealth jet in route,

make sure you are ready, the window will not be open long" the master explained. Lana nodded then turned away. The screen went blank, Lana then turned to the staff

in the control room. She pulled out her tablet "upload all server data to this, then purge it" the staff said nothing but turned and began typing frantically on their

keypads. Lana motioned to her Bisharps and whispered. "Take the pad to my chopper along with the staff, if the MRPA get anywhere close leave without me". The

bladed pokemon nodded. Lana then left for the elevator, the two assets were still unsecured and she needed to fix that. She pulled out her phone and called Ethan.

"Prefect what is it" Ethan asked in a rushed tone. "I'm on my way to cell block CD23, i need you and your team to secure the assets before i arrive, understood"? "Yes

ma'am" Ethan responded. Lana then hung up the phone, she had to hurry.

* * *

As Ethan arrived at the cell block he was greeted by his squad of soldiers. "Commander, we got the lab aids out,what are you orders" Sandman asked. "We're to guard

these cells until the prefect arrives" Ethan responded. Sandman nodded and spoke into his helmet."Granite, take up defensive positions". The other 3 members of

Ethan's squad spread out around the cell block.

As they were waiting for Lana's arrival Ethan thought about his team, they were closest thing he had to a family. Before the serum they were the doctor's greatest

achievement. They weren't shifters, but they were as close as it got. Sandman was Ethan's wingman, cool under pressure but wasn't afraid to crack a joke, he had

garchomp DNA giving him tougher skin and control over rock and other minerals. Truck was the brute force of the team, his Steelix DNA allowed him to turn his skin

into metal as tough as a real Steelix. His personality was the same as his skills, headstrong, loyal and thought with his fists. Frost was the silent one, only talked when

he felt he absolutely needed to, his weavile DNA made him quick and stealthy,perfect for a sniper. Lastly there was Grinch, the teams demo man and tech specialist. He

came off as grumpy, but that was mainly his electivire DNA getting the best of him. He gave off small shocks on accident due to anger at first, but he learned to channel

that electric knowledge into technology.

Ethan was snapped from his thoughts from a pressure in his head. Something was coming, and it wasn't Lana. Ethan put his hand on his sword ready for anything. "I

knew you were hiding something, but i didn't think it was this" said a cold voice. Ethan's eyes went wide as three people came around the corner, Connor, Alex and

Charlie followed by 5 MRPA soldiers.

* * *

Alex's POV

"You were a spy the whole time" i asked in disbelief. Ethan turned his head, i could feel his regret, he just radiated indecision. Before i could say more Ethan shook his

head and said "Granite, execute" the 4 soldiers leveled their rifles, but the bullets never fired. Connor held out his hand, screws and parts flew out of the guns, in

seconds they fell apart like a jigsaw puzzle. Everyone in the room went wide eyed, "you picked the wrong side Ethan" Connor said in a dark voice. With a wave of his

hand Ethan and the other Cipher soldiers passed out, hitting the ground with a defining thud. "Wha, how are you" i asked, too gobsmacked to speak. "Save Jake and

Cassie now, explanation later" he ordered. We then turned to the elephant in the room, the two cells. Connor closed his eyes, turning his head as if he was looking

around. He opened his eyes and pointed to the cell of the right "fireproof, as in COMPLETELY fireproof, you and charlie take this one. I'll take the other one" he said in a

dead serious voice.

Charlie opened the door, only to be met by a massive flamethrower. He directed the fire around us keeping me safe, thank arceus he went first. Once the flames parted

i saw our attacker. It was an Entei, a real living breathing legendary pokemon.

"Wait Charlie, Alex" said a voice in my head.

"Jake is that you" I asked in disbelief.

The Entei relaxed instantly, "yea its me" he said in a somber tone. I couldn't take it, i ran up and hugged him around his neck. "I was so worried about you" i said with tears in my eyes. I collected myself, stepped back and looked at him, he looked rough. His shaggy brown fur failed to hide multiple cuts and bruises, but he looked well fed at least. I shifted my hand into a lucario paw and cut off his shackles with a metal claw. "

I can't shift back with this collar on" he explained.

I nodded and tried to slash it off with a metal claw, but it merely bounced off. Charlie stepped forward and began to heat up the collar with his hand, then i grabbed the collar and pulled at hard as i could. Soon the collar cracked and split, falling to the ground with a ringing sound. A soldier handed me a shift suit and i laid it on the floor. We turned around and let Jake have some privacy to change back.

"Im good" he said, allowing us to turn around. It was good to see him back to normal, however his charcoal back hair was now a ghostly white, like the fire on an Entei's back. "Let's get outta here" i exclaimed.

We left the cell only to be met by Connor with a sad look in his eyes and a black pokeball in his hand. "Connor, what's wrong where's Cassie" i asked, fearing the answer. "She's in here, but there's a problem" he said quietly.

"What kind of problem, why did you catch her" Charlie asked timidly.

"She's gone, mentally, she's gone" he explained.

"That doesn't make sense, english please" i demanded.

"Cassie's mind is offline, that Raikou's nothing but a mindless beast" he explained further. Jake didn't say anything, but he didn't look surprised.

"You said she's offline, there has to be away to fix here right, right" i kept asking. Connor just shook his head and began to walk away. "

Let's just get the doctor" Charlie conceded.

* * *

We were running towards the doctor's lab when Connor yelled "hit the deck".

We all dropped to the ground, however the soldiers in front of us weren't fast enough, a ball of pink light wized over our heads and exploded. The four soldiers were zapped by the light and fell to the ground, dead instantly.

We all stood up and looked at our attacker, she was wearing a black suit with the Cipher logo on it. She gave a smirk and launched another attack, i was about to dodge when Connor stepped forward and

held out his hand. The ball of light stopped then dissipated instantly.

The woman eyes went wide, but then she smirked said "to think you were hiding all this time and you gave yourself away just to help these people" she chuckled.

Connor's eyes tightened "so you're his handler" Connor said coldly.

The woman laughed and said "indeed i am, it's been far too long brother dearest".….

 **DUN DUN DUUUUN**

 **Surprised? i hope at least some people were surprised.**

 **Follow this story, or if your feeling nice leave a review, i desperately need the feedback.**

 **i am still looking for a new beta reader. PM me if you're interested.**


	15. Chapter 15

Chapter 15

3rd person POV

"Wait, what" Jake asked as the confusion spread to everyone in the room.

"You seriously you didn't know, wow my little brother can tell a lie after all" the woman laughed.

"Connor she's joking right, right" Charlie asked.

Connor shook his head. He opened his mouth but he couldn't find the words.

"What's wrong Connor, scared that you're little secret isn't safe anymore" the woman taunted.

Connor finally found his voice "yes Lana, i am" he said forcing the words out.

Alex cocked an eyebrow "how is she your sister" he asked in disbelief.

"The doctor is still in his lab, don't let him get away" connor said dismissing his students.

"What, no we're not just leaving you" Charlie stated fiercely.

"If the doctor gets away this will all be for nothing, go that's an order" he barked

Connor tossed the black snag ball to Alex. He was caught off guard, but he understood what Connor was telling him.

Alex clipped the snag ball to his belt. He looked Charlie dead in the eyes and said "let's go"

The 4 shifters ran off down the hall, leaving Connor and Lana alone.

* * *

Connor's POV

"How can you just stand there and smirk, after everything you did" I asked quietly.

"Whatever do you mean" Lana said in fake innocence.

"You know what I mean, you know everything you did" I barked at her.

"Oh please, all I did was ensure my survival, and Cipher would have found us eventually" she jeered in response.

"Yea but at least we would have had time to mount a proper defense, did that ever cross your mind" I demanded.

She just laughed in response.

"Stop laughing, how can you be so nonchalant about all the death you incited" I yelled.

"Oh baby brother, always the soft one" her voice was rich with sarcasm.

"You watched as that man, who you now oversee, butcher, dissect and poison your own kind, your friends, your family, did you feel nothing when you saw that happening" I yelled with wet eyes.

"No I felt something, I felt sad, for you, because you picked the wrong side, I didn't know all that the doctor was doing" she said innocently.

"Cut the crap, I knew you were watching all of it, in fact I still remember seeing you" I revealed.

"Really, when did you see me" she asked curiously.

"It was 5 years after we were captured, you looked at me, I knew it was you. You looked at me, half starved and bruised in my cell and what did you do, what did you do" I demanded.

"I don't remember that" she lied again.

"You just looked at me for a fleeting moment, then walked away like I wasn't there, you didn't even have the gall to say anything" I screamed at the top of my lungs.

"I guess there's no fooling you" she conceded.

"I'm going to bring you in, you'll face justice soon enough" i yelled as confidently as i could.

"Oh brother dearest you know as well as i do that no cell can hold me" she snickered.

"Then I'll put you down right here" i yelled.

"Oh brother don't be so dramatic, do you really think you can bring yourself to kill me" she asked sinisterly.

The words hit me like a truck, not because of anger, because she was right.

"I'm leaving, you have two choices. Chase me even though you can't fight me, or help your friends who will definitely need it against the doctor's new powers" she stated firmly.

I said nothing.

"You may wanna think fast" she taunted.

* * *

Alex's POV

We got to the lab in record time. The room looked like a normal hospital, which didn't comfort me at all.

"Could Lana really not stop a few children" said a voice in our minds.

"Show yourself, or are you too much of a coward to actually fight" Jake yelled.

Then a man appeared from a flash of purple light. He definitely looked like a mad scientist.

"Ah you let the Entei off his leash" the doctor chuckled.

"You're gonna die for what you did to my sister" Jake screamed.

"Oh please, my powers are far beyond yours" the doctor said proudly.

"Oh yea" Charlie taunted.

With that Charlie shifted and launched a massive jet of fire. The doctor was completely engulfed in flames.

However the flames seemed to be withering and fizzling out, soon the flames parted and the doctor was standing there smirking, his lab coat singed around the edges but completely unharmed.

My jaw dropped, Charlie was just staring at the doctor gobsmacked.

"I'm in a hurry so let's just end this" he said as he raised his hand.

Suddenly I felt weightless as we were all lifted off the ground.

Before i could even think i was slammed to the ground, black spots clouded my vision as a horrible snapping sound came from my arm. I was too out of it to even feel pain. I blacked out soon after, my last memory being a felling of total helplessness.

* * *

Charlie's POV

I released a blast of fire, freeing me from the telekinesis. I landed on the ground, falling to my knees and panting.

"Still standing huh. I'm impressed" the doctor admitted.

"I'll keep getting up as long as I physically can" I yelled

"Good" the doctor hissed.

He threw off his lab coat revealing a black shift suit. Then his head transformed into a greyish cat like face. His arms thinned and his hands merged into 3 fingers with orbs on the end. Then a large purple tail grew and encompassed most of his lower body. Soon a fully formed Mewtwo was in his place.

I cloaked myself in fire and charged at the doctor. Before I reached him I shot a fire spin. He was soon surrounded by an isolated tornado of fire.

I ran through the fire kicking him in the chest and knock him back. Following that i threw fire punch after fire punch. He dodged and sidestepped as an incredible speed, however i faked him out with my left hand and punched him in the right cheek. Fist and talon met flesh as the doctor was given a huge slash on his cheek. He staggered back, clearly shocked.

I fell to my knees, even with the stamina of a Blaziken i was out of gas. The doctor lifted his paw and rubbed his cheek, a large red stain adorned his orbed hands. The wound then sealed itself, the healing factor of a legendary pokemon repairing the damage in seconds.

"All that for just a little blood" he scoffed as he walked up to me.

I said nothing as my lungs were burning from exhaustion.

"You have my respect, sincerely" the doctor said in a calm and honest voice.

He grabbed me by the face and said " sadly you never had a chance from the start, i know every trick and tactic you practiced thanks to Ethan" he said snidely.

"So he was a spy the whole time" i asked between pants.

The doctor nodded "indeed, but you've impressed me and i need to leave, so i'll let you and the lucario boy go" he said as he walked towards jake.

"However the Entei and the Raikou are coming with me" he said as he retrieved the black snag ball from Alex's belt.

I tried to stand up but fell to the ground again, i had nothing left.

"Till we see each other again" the doctor said as he levitated Jake off the ground.

He began to walk away, but then a new voice came from the other side of the room.

"Herr Doctor" Connor said in a icy tone.

The doctor went wide eyed as he dropped Jake and looked at Connor. "It can't be, your dead, that entire facility was turned to ash" he yelled in disbelief.

"It ill take a lot more than a little fire to kill me" Connor said with a brutal scowl on his face.

The doctor shot a blast of electricity of Connor, but the bolt of lightning had no effect and he simply walked forward.

The doctor raised both of his hands and used telekinesis on Connor, the psychic wave was so powerful it was cracking the metal floor around him. Strain was all over his face as he tried to push Connor back, but nothing happened. Connor pressed forward and punched the doctor in the face, knocking out a bloody tooth in the process. The doctor fell to his knees, dropping cassie's snag ball as he clutched his bleeding jaw.

Green energy surrounded Connor's hand. He slashed at the doctor, fully intent of ending his life. The killing blow never came however, the doctor teleported away in the nick of time. Connor's hand impacted the floor creating a small crater and a deafening thud.

"Coward" Connor scoffed

I got up and shifted back

"You ok" Connor asked as he tossed Cassie's snag ball to me.

"I'll live, you" i asked in response.

"Im fine, let's get the others and leave" he said in an nonchalant voice.

Despite his seemingly casual demeanor i knew he was bothered by something. I decided not to push him for answers, we needed to worry about Jake and Alex right now.

We were able to get Jake to his feet, but alex was a different story. His arm was twisted into a grotesque shape, he could barely stand due to the pain.

Connor lifted alex up and threw him over his shoulder. "Let's get out of here" he grunted.

 **Apologies for the long wait, finals are coming up and that really kills my free time.**

 **Leave a review, I really would appreciate it**

 **Ps**

 **I've decided to beta read on my own so don't worry about that.**


	16. Chapter 16

Chapter 16

3rd person POV

As Connor and the 4 shifters emerged from the factory they were swarmed by medical personnel. Alex and Charlie were carted away for proper care leaving Jake and Connor alone. As soldiers and medics hustled around them Jake looked at the black snagball in Connor's hand.

"What now" Jake asked in a hollow voice.

"I have some friends who may be able to help her, but only i can go" Connor said as Michael and the professor arrived on the scene.

"Im not letting you take my sister anywhere" Jake snarled.

"Well it's that or have her locked in a cage the rest of her life" Connor responded bluntly

"I think you should listen to him Jake" Michael chimed in.

Jake shook his head, but then paused. He was silent as he tossed around ideas in his head.

Finally he spoke "go, do what you can" he conceded.

Connor gave a weak smile and clipped the snag ball to his belt, he turned to the professor and said "fill them in about me"

Andrew nodded quickly in response.

Connor was enveloped in a bright flash. When the light subsided there was a Pokémon in Connor's place. One Jake had never seen before,one that was only referenced in myth.

It looked like a mix between a dragon and a jet plane. Every single part of its body looked aerodynamic and sleek. It had a grey neck and small arms with claws on the end. It was bright green with red eyes.

Before anyone could say something the Latios shot up and flew away. Before it was out of sight a small cloud appeared around it with a loud boom. Then it disappeared into the distance.

* * *

Connor's POV

I arrived in altomare in 2 hours later. I could've gone faster, but an object traveling faster than Mach 2 was far too conspicuous.

"Norin meet me in the garden's water entrance" I said via telepathy

"Why are you back so soon" he responded

"I'll tell you later" I said before ending the connection.

I gathered every empath I could find. Cassie's mind was so damaged I had my doubts whether or not they could do anything. I opened the snagball and released the raikou. The first thing I saw was the eyes of a beast, nothing remained of the kind girl from a few weeks ago. The raikou began to move but the empaths quickly subdued it with hypnosis.

"We'll see what can be done, could you leave while we work" one requested.

I nodded and left. I needed to think, alone.

* * *

I always knew my sister was probably alive, but I never imagined she was the master's prefect of all things.

I sighed as a jet roared below, how humans tolerate those massive engines I'll never know. I was at least 40,000 feet up, I always just flew when I needed to think, the rushing air was always soothing to me.

I knew that my sister was a monster, she was too far gone to help, but even when innocent lives were on the line I just couldn't bring myself to fight her. She was a good person once, many years ago.

Those memories of what she used to be was just too much, but I had a nagging feeling that one day, I would have to put her down. I just prayed that day never came.

* * *

Jake's POV

The professor brought us to his office, we all sat down as he looked out the window, he looked outside longingly. He was deep in thought, pondering something. He finally turned to us and said "you all must have questions, and now I'll answer all of them. I expect many of them are about connor, yes"

We all nodded as he sat down. He rubbed his forehead and said "it's time to tell you a story, one that began 35 long years ago"...

 **Author's notes**

 **sorry about the short chapter and the long wait, rest assured the chapters will be back to normal next time**

 **leave a review please**


	17. Chapter 17

Chapter 17

 **Authors note- the following chapter takes place 35 years before the events of chapter 1**

3rd person POV

The sun was just over the horizon, and a small group of lati were arriving from a late night hunting trip.

They arrived at Eterna forest and began dividing up the fish. The entire herd was soon gathered and began eating. This was a bountiful catch, the leftovers were enough for a week of food.

During the feast the Alpha noticed his daughter was absent from the herd. That was unusual even for her. His daughter was always the antisocial one, but he loved her all the same.

He and his mate were a rarity among their kind. While most lati are a purebred of one of the 7 body types or a hybrid of two with limited abilities of both parents they were neither. They were a incredibly rare example of a prefect hybrid. Perfect hybrids had the full power of both body types they were descended from. This made them stronger than both parents combined.

His mate was a perfect hybrid of a shade and a changeling.

He was even more rare than that. He was the pinnacle of a skydancer, an empath and a feral. A perfect hybrid of three body types had never been recorded, but he was proof that they existed. He was abandoned while he was an egg, the only remnant of his family was a necklace with a rare stone in it.

He knew his children had inherited his powers, along with his mate's. They may even be the most powerful lati in history. He just prayed that they would not be hunted for it. Their powers were a well guarded secret though, only he, his mate and her sister knew the truth. While each of them had the same abilities they always seemed to prefer some over others.

His son Connor had the wingspan of a skydancer and the strength of a feral, along with the perfect cloaking and phasing of a shade, he was easily identifiable by his rare green feathers.

His first born, Lana was a near polar opposite to her brother. While Connor had many friends and was a energetic youth Lana preferred to keep to herself, she was offend seen as cold and obsessive, part of that was the traits of her mixed heritage. Unlike Connor she loved her extra abilities. She had incredible psychic powers, on par with a changling three times her age. Her illusions fooled all but the most skilled minds. However what was troubling about her behavior was that she was caught controlling minds of other Pokémon a handful of times. Such abilities were not allowed to be practiced by anyone in the herd. Lana was definitely more inconspicuous than her brother. She could be identified however by her smaller teeth and muted red feathers.

Eventually Lana join her father and ate her food, however she seemed troubled. She was looking at the ground and nothing else. She was purposely avoiding any and all eye contact.

"Lana, what is troubling you my daughter" her father asked.

She shook her head in response, still avoiding her father's gaze.

"Please Lana, tell me what is bothering you" he said kindly

Lana then spoke in a whisper, it was so quiet that even the sensitive ears of a latios could barely understand it.

"I'm sorry" she whispered

Before her father could even begin to guess what she was apologizing for he felt a pain in his side. Something small was poking into his skin.

Suddenly the world was spinning and he fell to the ground, too weak to levitate from the drug. He lost consciousness as screaming erupted around him.

Out of the trees came humans in armor, holding dart guns and nets. The entire herd was sedated or ensnared in less than two minutes.

The hatchlings were simply grabbed or caged as most of them were too young or shocked to defend themselves. Only one youth put forth an effort to fight. A green blur rammed into a soldier knocking him to the ground. The small dragon was kicked to the ground by another soldier. The desperate youth attempted to get airborne but was subdued by a rifle butt to the back.

Connor watched as his herd,friends and family were dragged to the human's flying machines. Those who fought were beat into submission. No one escaped, but one lati was simply left alone. Lana was the only one who remained safe.

She was approached by a tall human in blue robes. He commanded respect among the soldiers, who did not dare meet the gaze of his dark glasses.

"Well done little one, you have cipher's thanks. Please come with me" the human said kindly.

"Lana help me" Connor cried to his sister.

Lana turned to face her brother, her eyes were a void. Nothing, no sadness , no satisfaction, and no remorse.

She turned back to the human and followed him to his flying machine.

Connor was stunned, the big sister he looked up to, cared for and trusted more than anyone else had just betrayed not only her family, but her entire herd…..

 **Author's note**

 **thanks for all the views. Please leave a review and follow this story.**

 **The next chapter will be the rest of Connor's history then we will be back to the main plot.**

 **Special thanks once again to** **Storylover Vodhr- Dux Ducis for letting me use some of his ideas. Check out his story dragonfall**


	18. Chapter 18

Chapter 18

 **Author's note- Most of this chapter takes place 28 years before the events of chapter 1**

Chapter 18

Connor's POV

I tossed ideas around in my head as I ate the usual slop in my cage. This was it, this was the day. I just have to find a way to get everyone out, not just me.

I had been practicing my illusions for months. I was finally able to look and feel like a human.

Before I could finish my thoughts a voice appeared in my head. One I had not heard in 7 long years.

A human was standing mere feet from my cage. I knew here eyes all too well.

"Connor, how would you like to get out of here" my sister said.

"Lana get out of my sight" I barked at her.

"Relax I'm here to help" she said in a kind voice.

"Help me" I said slowly

She nodded

"How can you live with yourself, how can you stand the fact that your friends and family are being butchered by that doctor" I asked her, enraged.

She shook her head and walked away.

Before she left she turned and looked at me one last time. She had genuine sadness in her eyes.

Then she disappeared from my view.

3 weeks later

I was still planning my escape when I felt a presence in my mind.

"Connor, can you hear me" my father said

I couldn't take it, tears poured from my eyes.

"I love you my son, I have sent you a gift with help from your mother. We both love you so much". He said as a small necklace appeared in my cage.

"Dad where are you" I begged.

"Me and your mother are in the doctor's laboratory. This is it for us" he explained.

Thanks to the psychic link I could feel the sorrow and fear he felt.

"No dad please" I

I begged as the link began to weaken.

"Stay strong my son, survive, never give in to these horrible humans, and live, I beg you live" he said.

Then I felt a pain in my chest, my father had just been cut by a knife.

"I love" he said as he breathed his last. The link disappeared, and I was alone once more.

I couldn't do anything but weep all night. I was too broken to even think.

The next day I resolved that I had to escape. I put the necklace on and said " give me strength dad"

Suddenly a massive boom hit my sensitive ears. Sirens blared as a voice said "attention, security has been compromised, proceed to your designated exits. Self destruct in 5 minutes"

I began to headbutt the cage, but it didn't even make a dent. Nonetheless I kept trying.

"Self destruct in 3 minutes"

"Think connor think" I yelled

Then it hit me. My cage wasn't supertangable like the cages for shades.

I concentrated as the sirens blared even louder

"Self destruct in 1 minute"

I finally phased through the cage and blowed open a hole in the roof with luster plurge revealing a long tunnel with light at the end

10

I focused all the energy I had in my wings, I hadn't flown in years but it was now or never

9

I managed to get airborne, my wings were sore from years of being in cages

8

I powered through the pain and flew through the hole

7

I flew through the tunnel, the light was getting closer.

6

I had to get above ground

5

I pushed everything I had left into my wings

4

A small cloud formed around my body as the light got brighter

3

I tasted fresh air for the first time in years as snow blew around me

2

With a deafening boom I broke the sound barrier, gaining altitude at an mind numbing pace.

1

A massive explosion erupted from the mountain, causing an avalanche.

I found a place to land, I was completely exhausted.

I fell to the ground and blacked out.

When I came to I was partially covered in snow. Luckily no one had seen me land.

I weakly hovered above the ground.

The frigid air was soothing. At long last I was free.

However that happiness was short lived.

Then it hit me. I was the only one who escaped. Everyone one else, my parents, my friends and my entire herd was gone.

I shook my head, I had to live, I had to live. I just kept telling myself that.

My mom once told me she had a sister who left the herd and went to altomare, some island near jhoto that apparently had a lot of lati there.

I suppose that was the best place to go…..

* * *

 **Author's note- back to the present**

Alex's POV

The entire room was silent as the professor finished the story, he explained that he met connor a few years later and earned his trust after healing a wound he had acquired from helping save Pokémon during a forest fire.

"So that's why he didn't want to take the doctor alive" Jake said quietly.

"Indeed, connor may seem cold, but he has a good heart. He's hard on you guys because he wanted you to be ready for cipher" the professor explained.

Jake shuffled in his seat and asked "so he took my sister to altomare"

"I assume, some of the lati there are excellent healers" the professor guessed.

"So what now" I asked.

"For now rest, you all have been through a lot in the last few days. I'll tell you as soon as I hear from connor about Cassie.

We all nodded and left the room, we were all tired, physically and mentally.

We walked to the dorms together in silence. We were still processing what had happened in the last few days.

I entered my room and flopped down on my bed, too exhausted to put on my pjs. I was out cold within five minutes.

We may have won today, but cipher was far from done. This was only the beginning….

 **Author's note- thanks for all the views**

 **Supertangable cages are something cipher designed to stop shades from passing through walls**

 **Leave a review and tell me what you think.**

 **Thanks again to Story Lover Vodhr Dux Ducis for permission to use his ideas**

 **check out his story Dragonfall**


	19. Chapter 19

Chapter 19

Connor's POV

I was on my way back to Cassie when an all too familiar latias stopped me.

"Hey Connor" she said shyly.

"Hey Lisa" I responded.

Lisa was my only other friend in altomare. She was perhaps the only latias I had feelings for. She wanted to be my mate, but I kept telling her time and time again I was not ready to commit.

I cared for her, but I refused to be with her for one reason, my special gene. If I were to have a kid with her, the hatchling would have the same curse as me. The extra powers that made me a target were not something I wanted to pass on.

"Connor I have something to I Need to tell you" she said in a whisper

"Can it wait, I have something I need to do" I said in a rush

"Well it's just that" she stuttered to say even that much.

"I'm sorry, I'll talk to you later" I said as I brushed past her and zoomed towards

Cassie.

* * *

As I arrived the empaths started moving away from Cassie.

"We managed to heal her mind, but there's a problem" one said coming forward.

"What kind of problem" I asked sternly

"She may, lose control sometimes" she said vaguely.

"Define lose control" I asked

"She may slip into this rage again, but only temporarily" she explained.

"Ok, thank you nonetheless" I responded

"She'll come to soon, I suggest you get her out of here, the elder says she cannot stay any longer.

I nodded and said "I'll take it from here"

The empaths soon left, leaving me alone with Cassie.

Now I just needed to get her something to wear.

* * *

Cassie's POV

I woke to a pounding headache, did the doctor sedate me after. Then it hit me, my mom was dead, my adopted mom who I knew since I was 8 was dead.

I looked around to see that I was in an alley, not in a cell. That was a positive.

"Took you long enough" a familiar voice

I snapped my head towards the voice only to see Connor in front of me. He had a kind smile on his face.

"Stay back, this is a trick isn't it" i asked cautiously.

"Cassie it's me, I got you out" he said slowly.

He began to walk towards me, he had a duffle bag on his shoulder.

"I said, STAY BACK" yelling at him.

I began to build up an electric charge, and bared my fangs ready to zap him if he didn't back off.

"Cassie, you're last name is Anderson, you trained with your brother, your hate bug types, especially Beedrill" he said with his hands out in front of him

That convinced me, only Jake and Connor knew that.

"You can shift back now, I got that collar off" he said as he dropped the duffle bag in front of me.

He turned around so I could change back in private.

I shifted back, it felt weird as I was shrinking instead of growing. Then I put on the clothes in the bag. They were a little big, but I didn't mind. My body was so stiff from being a rakiou for weeks.

"I'm good" I said, allowing Connor to turn around.

"Did you find my mom's body" I asked him

"What do you mean , she's alive and well"

"I saw her, that woman with the red hair, she she" I couldn't say it.

"What you saw was an illusion, nothing more" he explained.

I ran up to him and hugged him, so happy to know she was alive.

"Ready to go home?" He asked me

"Um how are we getting there" I asked.

"I need to do something real quick then I'll show you" he said

"I'll just stay right here" I said.

"You could walk around a little bit, cipher won't find you here" he reassured me.

"I'm not so sure" I said

"Eh your choice" he said

With that he turned away and walked down another ally.

I decided to just sit on a bench and enjoy the sunlight and fresh air, for the first time in weeks I was at peace.

* * *

Connor's POV

I entered the garden only to see Lisa waiting for me with a nervous smile on her face.

"What is it, what's wrong" I asked concerned for her.

"Connor, remember that night when my mom died and you spent the night with me" she said quietly.

"Yea" I responded

"Well um we uh got a little too close" she said vaguely.

How could I be so foolish, I never considered the possibility of it happening.

"I'm pregnant, the egg is due is about a month" she said forcing the words out.

"I'm sorry I should have told you sooner" she apologized.

i was dumbfounded, so many problems and scenarios rolled around in my head as my minds went into panic mode.

i turned around and promptly lost my lunch

"I love you please help me" she begged.

"I love you too" I responded.

i then closed my eyes, I shook my head and finalized my decision.

I then focused my psychic into my fangs, then I bit her ear, claiming her as my mate.

* * *

Cassie's POV

When Connor returned he looked like he had seen a ghost, not like a ghost type, an actual ghost.

"What happened" I asked

"Nothing" he lied

With that there was a flash of light and a green latios appeared in front of me.

My jaw dropped,

"Hop on" he said via telepathy.

I gingerly climbed onto his back, his feathers were sleek and rigid to the touch.

"Put your arms around my neck and hold on" he requested.

I did as he asked.

In an instant he blasted off, we reached 15 thousand feet in a few minutes.

"We'll have to take it slow, I don't wanna get near a jetliner, we'll be in Veilstone in about 6 hours" he explained.

"6 hours, can't you go faster " I complained.

"Sure if you want constant motion sickness and oxygen deprivation " he joked.

* * *

3rd person POV

The room was massive, cipher banners hung on the walls and massive stone pillars stood in a line leading to the back of the room.

It was dimly lit, only small lights on the walls allowed for meager visibility. The room itself had a purple carpet leading to the throne.

Six bisharps were stationed around the throne, their metallic eyes constantly trained on the two visitors that were prostrate before the master.

Lana and Gregavich were exchanging glances, but were too nervous to say anything.

"This day inflicts a heavy toll, until the alola factory is completed we have no way of producing shadow Pokémon" the master said in his ever calm voice.

"My most sincere apologies master" Lana said as the master studied her, his eyes invisible behind his dark glasses.

"You could not stop that skydancer, for all that bravado you are a…" Gregavich was cut off by master before he could finish.

"Silence doctor, neither you or Lana are at fault for this setback, stand up the both of you" he commanded in a slightly louder tone.

Both of them looked extremely confused, as if the master had just said something in another language.

"You were not prepared for the Lugia or the latios, two variables completely unknown until they appeared, we must simply move on and continue where we left off" he explained.

"Doctor, go to Alola and oversee the completion of the new factory" the master ordered.

The doctor nodded and said "it will be done Master".

The doctor turned and left, leaving the room without saying another word.

"Lana, Victor will be overseeing the doctor's work from now on, I have no patience for you and him bickering like children" the master said coldly.

Lana bowed her head, the doctor's ego was the problem, not her, but she did not dare argue with the master.

"I need you to stay here, with Victor gone and Nikolai training Ethan's team I need someone to keep an eye on the projects here at HQ. Also do not lie to me again" he requested.

"Forgive me, my brother caught me off guard and I did not feel that it was the time to make a stand" she admitted.

"You chose wrong, I expect better from my prefect" he said harshly

"I will do better master" she said, her voice completely devoid of emotion.

"Excellent, you may leave" he said motioning to the door with his hand.

Lana bowed then headed to the large door at the other end of the room.

"And Lana" he said before she could leave.

Lana turned to face him once again.

"Do not fail me again, if you see your brother, you kill him" he ordered

She paused for a moment, considering what to say.

"Yes my master" she said with a smirk on her face.

 **Author's note- Dun Dun Daaaaa**

 **rest assured this will not turn into a ripoff of dragonfall, I did this for 2 reasons.**

 **1\. Give Connor a bigger emotional side**

 **2\. Have a reason to not have him around for a while as he's too strong for the challenges our other heros will be facing.**

 **Leave a review, I would love to know what you like about this story.**


	20. Chapter 20

Chapter 20

3rd person POV

As Jake, Alex and Charlie stumbled out of their rooms and headed to breakfast it seemed like any other day. As they sat down they all looked at each other and the reality of what had transpired in the past month finally hit them.

Jake had be tortured by mad scientist along with his sister and received powers he never wanted. His sister was a mindless monster that he may never be able to see again.

Charlie had gotten his own father arrested and then promptly joined Alex skydiving into a war zone only to fight against a organization that killed and corrupted Pokémon into living weapons and a being that's power brought any normal Pokémon or shifter to shame.

Along with the fact their teacher and friend turned out to be a 68 year old legendary dragon with a past more horrifying than they could have imagined.

"How are we gonna explain this to our parents" Alex sighed.

Jake and Charlie said nothing.

"I'm not quitting guys, I just hate to keep my family in the dark" he said defensively.

Before Charlie or Jake could respond the intercom crackled to life.

"Jake Simmons, Alex Mason and Charlie Daniels to professor Malcolm's office at once please".

The announcement made all three of them drop their food. This had to be about Cassie.

* * *

When they arrived they noticed that Connor was talking to the professor.

Jake opened his mouth to talk but the words never came as an all too familiar girl entered the room.

She looked the same, apart from her dark purple hair, the same color as a raikou's mane.

"Cass" he asked, his eyes foggy with tears.

The two ran towards each other, instantly joining into a hug.

"I thought I lost you" Jake sobbed.

The two stayed locked for a while before they finally separated and sat down next to each other. Jake and Charlie sat down beside them while Connor stood leaning against the wall by the professor.

"I know many of you didn't know that things would be this eventful or dangerous. I shouldn't have recruited you like that and I'm sorry" he said with his head bowed.

"I'm not going to hide anything else, from now on you all will know everything I know, and if anyone wishes to quit I will get you on the next flight home" he offered.

Alex shook his head and said "I'm not going anywhere, we have the powers to help people, and if Cipher wins there's no home at all"

Charlie looked at Alex and smirked.

"Couldn't have said it better myself" he admitted.

"We're staying too, we can't let Cipher hurt anyone else" Jake said with vigor in his voice.

The professor smiled, overjoyed that his students weren't giving up.

"I hate to damper the mood but I need to talk to all of you" Connor said causing every head in the room to swivel toward him.

"Cipher knows I'm alive now, I need to leave, I don't know for how long" he said vaguely.

"But we need you to train us" Alex stated firmly.

"Not really, I've reached the limit of what I can teach you, none of you are the same and I can't teach you anything else that isn't specific to you shift form" he admitted.

There was a brief moment of silence in the room. Connor had thoroughly won this argument in one statement.

"Before I go I need to talk to you two alone" Connor said pointing to Jake and Cassie.

"Why not all of us" Charlie interjected.

"It's a discussion about their new abilities" Connor said sternly.

Even the professor looked surprised,he looked to be in deep thought before nodding to Connor

With that he motioned for Jake and Cassie to follow, leaving Alex and Charlie behind.

* * *

In a flash of light Connor, Jake and Cassie arrived in a forest clearing, the dry autumn leaves falling around them and cracking beneath their feet.

"You two have a whole new set of problems" Connor said bluntly with his back turned to them

Jake and Cassie both seemed nervous.

"You both now have enough power to level cities and that's why you two need to train harder that you even have, but more importantly you both need to learn restraint" he said grimly

"But we know how to control fire and electricity, we were already doing that" Cassie said nervously.

"Yea but what was the effort needed to stun someone is now more than enough to kill someone" he said in a dark tone.

The two siblings said nothing.

"I've called in some favors and got some real Entei and Raikou to train you,they'll come to you when they are ready" he explained.

"Ok anything else" Jake asked, scared of the answer.

"One more thing, and this is going to be really hard to hear, but you deserve to know" he said.

"Well what is it" Cassie demanded.

"You two, well you won't be getting older very fast" he said, clearly forcing the words out.

"What do you mean" Jake asked, confused.

"Thanks to your legendary DNA you won't look 21 until you are least 100" Connor explained further.

Both of them went wide eyed.

"Long life has its disadvantages" Connor said bowing his head.

Jake and Cassie stood there in shock. They would out live their entire family, they wouldn't look like adults for almost 90 years, they could never have kids as they would outlive them and their kids kids.

"You two should go get some rest" he said as they teleported back to the school.

"I'm sorry" Connor whispered as he dropped his illusion and took off towards the setting sun.

Jake and Cassie simply went to bed without saying another word. Their lives had just been uprooted in an instant and there was nothing they could do.

* * *

As night fell a girl awoke in her cell. She was thin, clearly malnourished. She listened carefully making sure nothing was within earshot. She closed her eyes and focused on her hand. A frigid aura formed in her fist as she clutched the collar around her neck. The metal snapped from the cold and fell to the ground with a clang.

She then began to shrink slightly, her arms and torso turning pale and thin as he thighs became pink and round. Finally her forehead formed into a pink headpiece with three bulb like extensions on it, leaving a Medicham in her place.

She clutched a pinkish stone in her hand and with a flash mega evolved into Mega Medicham. She gathered energy and focus punched through the wall. Alarms blared as the cool breeze of Alola entered the cell. She jumped out, using psychic to cushion her fall. She then bolted towards konikoni city. She was free for now, but that would be brief if she could not get to the pier in time...

 **Author's note- I know it's been a while but my life has been Crazy recently.**

 **Leave a review and follow this story, it makes my day when someone gives me a review.**


	21. Chapter 21

Chapter 21

Author's note- 8 months have passed since chapter 20

3rd person POV

20 miles of the coast of Alola an unmarked freighter came to a halt. It's cargo, while mainly machine parts also included a select few test subjects that Dr. Gregavich had decided to bring with him to the new facility.

The facility was the pinnacle of Cipher's technology. A massive underwater factory that could produce 100 shadow Pokémon a week and had a large lab with holding cells and an arena fit for legendary Pokémon.

Today was the day the facility came online and Dr. Gregavich couldn't help but smile.

The doctor had been training extensively with his powers and even without shifting it was obvious. His skinny frame was replaced by a muscular physique that gave Victor a run for his money. Not only that but his psychic powers had increased his intellect to new heights. He could read 8 encyclopedias in a day and process information in milliseconds.

The freighter opened a number of doors on its underside and 5 submarines deployed. Unnoticeable by anything above they glided towards the facility and docked.

As the supplies were unloaded Gregavich was greeted by security director Kallahan.

"Doctor, welcome to triton station I'm" he was cut off but stood at attention all the same.

"Director Kallahan, head of facility security, joined cipher 3 years ago, headed the program to train new shadow Pokémon handlers and oversaw construction of this facility, completing it 2 weeks ahead of schedule I might add" Gregavich said, a hint of praise in his voice.

"I'm honored that you know me sir" Kallahan responded, somewhat stunned that Gregavich knew so much about him.

"As a cipher administrator it is my duty to know who I am working with, and those with talent" Gregavich complemented.

"Thank you sir, may I show you to your lab" he offered

"That will be unnecessary, I've seen the blueprints of this facility, but I wish for you to accompany me all the same" Gregavich requested.

"Yes sir" he said following the doctor.

As they were nearing the lab Gregavich stopped at the door to his study.

"You're study was prepared to you specifications" Kallahan explained to the doctor.

"Good, everything seems to be in order" the doctor commented as he sat down.

"Will there be anything else doctor?" Kallahan inquired.

"No, not for now but having a fellow shifter around is a welcome change of pace, you may leave" the doctor said as diverted his attention to a book on his desk. At that statement Kallahan nodded and left.

Kallahan shuddered as he left the doctor's study. He just seemed so unsettling, he had heard the stories about the doctor's new powers, he just hoped he would not see them firsthand.

* * *

As Gregavich finished his book the turned to a screen and pressed a button on the remote.

The dimly lit room was brightened by the screen as Ethan appeared, he was in full body armor and awaiting orders.

"Ethan have you found her?" Gregavich questioned.

"No doctor, but we have a fix on her location, she is meeting an MRPA operative in 3 hours" he explained.

"Proceed, if possible apprehend her before the MRPA arrives" the doctor ordered.

Ethan turned to cut the call but the doctor stopped him.

"Remember, I need her Alive, as little damage as possible, and do not make a scene" the doctor reminded him.

"Yes sir" Ethan responded as the call was cut.

* * *

Dana's POV

I hate subways. I know there useful but it's way too crowded.

I left the station and headed towards the cafe.

I didn't like trusting the MRPA, but it was them or cipher.

Cipher abducted me almost 2 years ago, they forced me to train. I tried to fight them but all it bought was pain. So I decided to play the part of someone who'd given up. Only when I trained enough was I able to escape.

Eight months on the run was hard, I had to steal and hitchhike to survive. I was originally planning to go home, but I eventually accepted that I couldn't because they were probably watching my house the second I escaped.

Then I heard about the MRPA, the people who were standing up to cipher. I wasn't going to blindly give myself over to them, but that seemed to be the only option.

I noticed the cafe was closed, it was only 5:00, odd but maybe they only served breakfast.

A chill went down my spine as something pierced my skin. I shifted instantly and used my psychic skills to dull the tranquilizer.

4 men in black armor appeared around me. I stated to get dizzy, the tranquilizer was still affecting me. I fell to the ground.

This was it, all my efforts had failed, I was going to be a lab rat for the rest of my life. As the soldiers reached for me they paused.

"Do you feel that truck" one said.

"It's boiling hot" truck responded.

Suddenly a ball of fire appeared in front of them. It dissolved and a massive dog-like beast was in front of us.

It was covered in shaggy brown fur with a gray plate, resembling a horseshoe mustache, covering its muzzle. A yellow crest with three sloped points on its forehead and red eyes that were trained right at the soldiers. Strangely to had what looked like a black suit over its body.

The soldiers were shocked. Before they could react a lucario wearing a similar black suit swooped down and blasted them to the ground with 2 well placed aura spheres.

The soldiers attempted to get up but the massive beast readied a fireball in its mouth.

"Stay down" the lucario threatened.

"You wouldn't kill us" truck taunted.

"Not you, but I might make an exception for you Ethan" the lucario yelled to the other soldier.

"You won't get a chance" Ethan remarked.

A grenade rolled into the street and a black smoke billowed out.

When the smoke cleared the soldiers were gone. The beast humphed and began to shrink. Soon a teenager with white hair was in his place.

The lucario shook his head and transformed into a teenager that was taller with black hair.

"You ok" the black haired teen asked as he helped me to my feet.

"Yea, I'm good" I responded.

"I'm Alex, and that's Jake" he said pointing to the white haired teen.

"You're the MRPA agents" I asked, stunned that they were my age.

He nodded and said "come on, let's go"

I followed them and we arrived at a parking lot that was empty.

Jake pulled out a phone and said "we got her, requesting a pickup" he said casually.

Soon a helicopter arrived and we hopped in. As the chopper took off I had one thing on my mind.

That was way too close.


	22. Chapter 22

Chapter 22

Cassie's POV

The smell of brewing coffee filled the air. I always visited the Perk when I had the time, it was refreshing to do something normal for once. Normal, my life was anything but that word now.

 **Author's note- italics mean flashbacks. And italics with underlining mean thoughts.**

 _We were walking through the woods at 5:00 In the evening of all times. Our new "teachers" were supposedly meeting us here. Connor had told us they were real Entei and Raikou. He expressed that this would be hard, but necessary._

 _We arrived in a clearing, the wind was swirling leaves around us. That combined with the setting sun painting the sky a beautiful shade of pink made a for a spectacular scene._

 _"So are they a no show" Jake asked, clearly still on guard._

 _At that statement a ball of fire materialized in front of us, the flames parted revealing an Entei. It was slightly larger than Jake's shift form, and its muscles were very apparent underneath it's shaggy brown fur._

 _Before we could speak a bolt of lightning struck the ground, causing us to jump back due to a primal urge of caution with electricity. Soon a Raikou appeared. It was sleeker than the Entei, its body clearly built for running._

 _"You are Cassie and Jake I presume" a deep voice said via telepathy._

 _We nodded._

 _"I am Ignitus" the Entei boomed_

 _"I'm Raiden" A younger voice said._

 _"Nice to meet you" I said shyly_

 _"If you would shift please" Ignitus Requested._

 _We both took off our outfits revealing our shift suits._

 _I closed my eyes and concentrated, I felt my muscles and bones grow as I fell on all fours. This was not painful however, in fact it seemed so natural now._

 _"Fascinating" Ignitus commented as I opened my eyes._

 _"What" I asked, puzzled._

 _"Despite being 17 years old your shift forms look around 400 years old" he commented_

 _"Wait that means were older when we shift" Jake asked._

 _"Yes, but 400 is roughly a teenager for us" Raiden explained._

 _"Well then, shall we begin" Ignitus asked us._

 _We both nodded, it was time to get to work_.

* * *

"Here you are ma'm" the waitress said, placing my coffee on the table.

"Oh thanks" I quickly responded, snapping back to reality.

"Your welcome, I really like your hair, who dyed it for you" She complimented.

"A former employer taught me" I lied.

"Oh, ok have a nice day" she said before walking away.

I picked up my coffee and left, I needed some fresh air.

As I left the Perk I sipped down my expresso, the sting of the strong coffee appealed to me. It seemed stronger than usual however, but I knew it wasn't the coffee. Ever since the serum I had shaper senses, better taste, better hearing and incredible night vision. All of these traits were easy to hide, but my dark purple hair was not. I had tried coloring it, but even that darkest black couldn't drown it out. I hated it, it was a constant reminder of my nightmares at the hands of the doctor.

" _If I ever see him again I'll rip his head off with my fangs, I must protect my pack"_

I shook my head at those thoughts, I clenched my fist, noticing small sparks around my fingers. Ever since I came back to the school I've been having strange thoughts, like a voice in my head. It always is angry or primal, like a wild Pokémon. I haven't told anyone, I'm not going to be called crazy, that's the last thing I need.

I was walking to my 2nd hour when a boy stopped in front of me, he didn't look friendly.

"Nice hair freak, why's it that color" he asked mockingly.

I remained silent and shoved past him, I had to stay cool, i was better than this.

"Too scared to say something" he taunted, following me down the hall.

I clenched my fists, sparks of electricity flying off my fingers.

 _I should rip him to shreds, he disrespected me, a legendary beast._

"No" I whispered. That's not me, I'm not a monster.

"Pathetic" he scoffed as he shoved me to the ground .

I felt my body changing against my will, my skin beginning to turn into yellow fur I was about to lose control again, but help had arrived.

"Get back NOW" a familiar voice said.

I felt a hand on my forehead, then a wave of soothing energy filled my body.

"Someone call the professor" a student yelled.

I managed to get on my knees, dizzy from a newfound headache. Only to be met by an instantly recognizable pair of golden eyes.

"Connor" I said, unsure.

"Hey Cass, can you stand" he asked, concern in his voice.

"Yea I think so" I responded, shakily getting to my feet.

"What did you do to calm me down" I inquired.

"Used my psychic skills to completely refresh your frontal lobe, essentially I just took a psychic defibrillator to your brain" he explained.

"What's happening to me" I said as the professor arrived.

"I'll explain, buts let's go somewhere private" he said in a hushed voice.

* * *

"I thought you said she was healed" Jake asked as he and Alex entered her room.

"She was, but the damage was worse than I thought" Connor admitted.

"Well can you help her" Alex asked.

Connor shook his head "I had the best healers in Altomare on it, and they just barley were able to stitch her mind together. They said that she just needs more time to heal" he admitted.

"Ok" I said calmly.

"So Connor, how long are you going to be around" Malcom asked

"I'm leaving tomorrow evening, then I'll be back for the PWT" he explained.

"Wait the Pokémon World Tournament is being held HERE" Alex said, clearly shocked.

Malcolm smiled and said"I was just about to tell you all. Not only is Veilstone hosting the tournament in 3 months time but you're all invited to be in the VIP lounge with me"

"Can I participate" Alex spoke up.

"I thought all you had was an Eevee" Charlie questioned.

"I was just starting to raise him, but I've got the 8 badges of Johto" Alex stated proudly.

"Why didn't you go to the league" Jake asked.

"I did, lost to that dark type chick, what was her name, oh yea Karen" Alex said.

"Wait, so you got to the last elite four member and you just gave up" Cassie asked.

"I was 15, decided to take a step back and train some more, by the time I was ready, it was time for high school" Alex explained.

The professor's eyes went elsewhere, he was clearly thinking long and hard about Alex's request.

"Ok, the qualifier is in 2 weeks, I'll get you signed up, you should do some training in the meantime" Malcolm recommended.

"I'll go to the PC" Alex said as he rushed out of the room.

"All of you get some rest, we'll discuss the tournament more in detail tomorrow" Malcolm said dismissing us.

We all nodded and left, things were finally looking up for us.

* * *

Kallahan's POV

"You wanted to see me doctor" I asked as I entered his study.

"Ah yes, please sit" he offered.

I obliged as he closed the book he was reading.

"We have learned the location of the Pokémon world tournament this year, it will be held in Veilstone city" the doctor explained.

"Why does a tournament concern us" I asked.

"Cipher doesn't exist anymore, the majority of the world believes we are long gone. This will be our opportunity to announce our return, while demonstrating our power" Gregavich said proudly.

"Very well, how can I be of aid to this operation" I responded.

"You can keep production going smoothly and prepare XD002 for its first test" Gregavich responded.

"Will all due respect, the shifters we have had trouble with are in Veilstone, what if they snag XD002" I questioned.

"A valid point Kallahan, but I've already made a solution to that problem, I'll brief you on the finer details soon, in the meantime continue doing what you've been doing" the doctor ordered.

"Thank you sir" I said as I stood up and left his study.

Soon the entire world would know that cipher was back, and stronger that ever.


	23. Chapter 23

Chapter 23

Alex's POV

"Typhlosion fire blast" I yelled.

A massive ball of fire erupted from his mouth, it then formed into a kanji and exploded on impact with the venusaur.

When the smoke cleared the venusaur was on the ground, swirly eyed and unconscious.

"Venusaur is unable to battle, Typhlosion is the winner" the referee yelled.

"That does it for the last match, Alex is the victor and our final qualifier for the tournament" the commentator exclaimed.

"Take a rest buddy" I said recalling my starter.

* * *

As I exited the arena I was greeted by Connor and Charlie, along with Dana.

"Nice job" she complimented.

"Thanks" I responded.

I then noticed Jake and Cassie were absent from the group.

"There off training" Connor explained in hushed voice.

"Oh" I nodded.

"Let's get something to eat" Charlie said.

"That's a great idea, I just flew a few thousand miles and I'm starved" Connor admitted.

Dana wore a confused look at that remark.

"Connor's not a shifter, he's something else" Charlie said.

"Keep it down" Connor reminded.

"Sorry, sorry" Charlie apologized quickly.

Connor smirked and said "it's okay, just be careful"

I motioned for them to follow and said "I know a good Alolan place, come on"

"Go on ahead, I need to check on Jake and Cassie" Connor said as the others began following me.

I turned around to acknowledge him but he dissolved into nothingness, followed by a whoosh of air from him taking off at high speed.

Dana's jaw dropped

"He does that sometimes" I joked as we headed to Main Street.

* * *

Jake's POV

"Now, let's try something new" Ignitus said as I came back from my 8 mile run.

"Ok, what" I asked still panting.

"You see we Entei have a move only we and Ho-oh can learn, sacred fire" he explained.

"What does it look like" I said as I got my wind back.

Ignitus gave a smirk and motioned his head towards a rock about 30 feet away.

He tensed his muscles and an aura of blue fire swirled around his fur He then opened his mouth and unleashed a massive ball of blueish white fire. The rock was completely enclosed by the searing fire. You could feel the heat even from 30 feet away.

When the fireball dissolved the grass was gone, the soil that had been turned to glass was all that remained.

"It's a powerful move, in fact I have only seen one move that was stronger" he added.

"What's that" I asked.

"Connor's luster plurge, its power is unreal" He admitted

"Wait Connor is THAT powerful" I asked

He smiled and said "Oh yea, when cipher had cornered my pack, Connor destroyed all their tanks and disarmed every soldier within 5 seconds, he was moving so fast that even legendary Pokémon couldn't see him. He could challenge almost any legendary and win."

My jaw was hanging open

Ignitus shook his head "The reason he never shows what he can do is that he's scared, scared that using all that power will corrupt him like it did to his sister. I doubt anyone has seen the upper echelon of his powers"

"Why did he help you then, if he's scared of what's he can do" I said

"He's got a good heart, he's too nice for his own good sometimes, that tough guy facade is just to hide how broken he is inside" Ignitus explained.

"What do you mean broken" I asked

"He's lost everyone he loved, friends family, his only blood relatives are his cousin and his psychopath sister. Losing that much takes a toll on anyone" he said quietly

"Were done" Cassie yelled as she approached, already shifted back.

"That appears to be the end of our lesson today, next time I'll teach you sacred fire" he promised.

* * *

As we were leaving the woods, Connor appeared in front of us. The moonlight shining off his green feathers.

"Care for a lift" he offered

We both nodded and hopped on, he gave a smirk and said "hold on"

Jake held on to his neck, and I held on to Jake' waist. We nodded and he took off.

* * *

We arrived at the restaurant, only to see the others leaving.

"Oh come on" I exclaimed.

"Sorry man, we waited as long as we could" Dana apologized.

"We got you some take out though" Alex said revealing a few to-go boxes.

"Thank Arceus, I'm starving" Cassie said.

We then sat down outside the restaurant and ate our food. I felt so happy, just sitting and chatting made me smile. This was the best night I'd had in quite a while.

I turned to face Alex only to notice Connor's absence form the table.

"He went to see the professor" Charlie explained.

I nodded and went back to eating, I just wish Connor would relax a little more.

* * *

3rd person POV

Malcolm was at his desk when the door opened, he looked up to see Connor with a frown on his illusionary face.

"Your early, I said that this wasn't urgent" Malcolm commented as Connor approached a bookcase in his office.

Connor waved his hand in the air, all the blinds shut and the door locked.

"You're a terrible liar, what do you need to tell me" Connor asked impatiently.

Malcolm closed his laptop and said "Cipher is planning something, there going to attack the tournament, during a match most likely"

"Then why not call off the tournament" Connor demanded.

"I can't, it'll cause public unease, we cannot scare people by calling off the tournament in light of a terrorist threat" Malcolm admitted, you could feel the anger in his voice.

"So what do we do" Connor asked.

"We prepare for the worst, I want Cassie, Jake, Dana and Charlie with their Snag Machines concealed and shift suits on in the stands. They need to be ready for anything, and Alex needs to be ready with his shift suit on and his Snag Machine close by" Malcolm explained.

Connor nodded.

"As for me, I need to be here, keeping an eye on the vault during the entire tournament" he said quietly.

"Connor, if anything goes wrong, keep them safe, even if it means revealing your true appearance, you understand" he requested.

Connor looked away, clearly thinking through the situation. He then looked at Malcom with determination and nodded.

"Thank you, fill them in discreetly" Malcolm whispered.

Connor nodded and turned to leave.

"You know I still see you as my son, if you need to talk, I'm here" Malcolm offered.

"I know" Connor said as opened the door and left. Leaving Malcolm to his thoughts.

* * *

3rd person POV

As the elevator opened Gregavich smiled. Before him was cipher's greatest achievement. The ultimate shadow Pokémon that far outclassed XD001.

XD-2 was not his achievement, Lana was credited with its creation and she was adamant about entrusting it to the Triton station's care. She begrudgingly agreed after the master had assured her it would not be tampered with.

The beast was asleep for now, it was always sleeping when not being used. Gregavich had decided to not disturb it until the week before the tournament. That way it would be at full strength for its grand debut.

He mused on the upcoming attack, while the MRPA was busy with XD-2, Nikolai would infiltrate the vault and retrieve the artifact, then the real work would begin.

Soon the entire world would know that Cipher has returned, and that no one, not even the MRPA, could even hope to challenge them.

 **Author's note- we have officially surpassed 2,000 views and I couldn't be happier. Thank you guys so much.**

 **leave a review if you'd like, I'm curious what you all think Xd-2 is**

 **My only hint is that it's a legendary Pokémon that many people can't agree on how to pronounce its name.**

 **See ya next chapter!**


	24. Chapter 24

Chapter 24

GLana's POV

"Hello Doctor" I said as I entered the command center.

"Lana the attack is in a few hours, shouldn't you be with XD-2" he said with his back turned.

"The master decided that I should retrieve the orb, Malcolm won't just hand it over" I told him.

"Fine, just do your part" he said as he pecked on his tablet.

"What are you working on Doctor" I asked.

"Double checking my insurance policy against the shifters, even with the radio frequency to stop their snag machines I need to be sure" he said impatiently

"Good, I can't have my favorite pet getting purified" I said.

"I'm preparing everything here, get to your position" he barked.

"Fine, play with your toys doctor, just make sure they work" I taunted.

* * *

Alex's POV

I stood atop the trainer platform as the opponent took their place. This was it, I had made it through the the entire PWT and I had a chance to battle lance if I won. Only one trainer stood in my way.

The crowd was on their feet, some cheering me on, some booing me, but I had learned to tune out the noise.

"Welcome everyone to the grand final, today we have two amazing trainers. In one corner we have a rising star, Alex from Goldenrod city. His opponent, the two time winner of the kalos league and a former champion, Calem from Vaniville town" the announcer roared.

I looked across at my opponent, he looked slightly older than me. He had short brown hair, a red cap with goggles above the bill and simple cargo pants.

"Now for this match we have a modifier, only one Pokémon is allowed,and the battlefield is a different one then last match" the announcer revealed.

The audience quieted slightly, these modifiers were hardly ever helpful.

The metal plate over the battlefield opened revealing a pool of water, with only a select few platforms.

This was not a pleasing sight for Calem, his poker face shattered for a moment, but soon reformed.

"Now let the battle begin" the announcer yelled , igniting the crowd.

I then picked a pokeball from my belt and tossed it in the air, I decided to take the natural choice for this battlefield.

A massive blue scaled Pokémon emerged from the pokeball. It resembled a giant horsea.

Calem smiled and threw a pokeball in the air. It opened revealing a massive gyarados. However what seemed unusual was a massive gem strapped to its head via some kind of mount.

"Kingdra Dragon Pulse" I ordered.

"Gyarados, dragon dance" he said calmly.

The multicolored beam hit dead on, the gyarados clearly felt it but remained steadfast and used dragon dance.

I shook my head and said "kingdra use rain dance" it was time to change tactics, dragon dance would make this fight a slippery slope if I didn't end this quick.

Cassie's POV

I watched the match concerned, Alex was definitely faltering, I just hoped he made a comeback.

"That stone is the endgame, Calem is just waiting to use it" Connor muttered.

Before I could comprehend Connor's explanation I heard a boom, something was coming.

"Get you snag machine ready" Connor yelled as the crowd went silent.

* * *

Gregavich's POV

I went to the roof with Kallahan , it was time for the main event.

"Today, we show the world our true strength Kallahan, perhaps it will give you some as well" I told him.

Before he responded a giant black serpent flew overhead, XD-2 had arrived.

* * *

Connor's POV

"Holy shit" Charlie said, gobsmacked.

The beast roared and began shooting dragon pulses all over the stadium.

Cassie, Charlie, Dana and Jake all jumped the barrier, intent on snagging the beast, however they then fell to their knees, as did Alex.

A sound hit my sensitive ears, it was so muted that I could barely even register it.

All of them were on the ground screaming and covering their ears, violent spasms overwhelmed their bodies. The entire team was down, I was the only one left.

I dropped my illusion and turned invisible, I had to stop that signal, now.

The stands were utter chaos, everyone was fleeing for the exits. The handful of security guards were overwhelmed.

I then noticed a flashing light in the announcer's box. I flew up at a rapid pace and discovered the source of the problem.

The announcers were gone, but the loudspeakers were still active. I acted quickly, using psychic to completely crush the panel.

I heard a roar, i turned around mid air. I then saw everything in slow motion, rayquaza was charging a dragon pulse, it was about to kill the entire team.

I moved at Mach speed, I was in between them and the beam in nanoseconds.

I poured my psychic energy into a barrier, forming just as the beam hit.

Charlie's POV

As my senses returned I looked up to an unbelievable sight. Connor was holding back the rayquaza's beam, on his own.

"Get to the school, the professor needs help" he said telepathically.

"What about you" I questioned.

"Go, NOW" he yelled as the others stood up.

We all turned and ran, Connor wasn't joking around, he needed us to go.

I just feared he wasn't capable of winning against such sheer power.

* * *

3rd person POV

Lana entered the vault via phasing, she had decided to be discrete.

She entered the vault, the adamant orb was sitting on a pedestal at the other end of the massive room.

She uncloaked and floated towards the orb, it was all hers.

She was blasted to the floor out of nowhere. A gallade wearing a black shift suit appeared in front of her.

"Ha, you think you can beat me old man" she scoffed.

"No, but I'd rather die than let you have it, this orb was kept here for a reason" he said defiantly.

I then noticed a small gauntlet on his bladed arm, with a jewel in the center.

He closed his eyes, a surge of light enveloped him, leaving a mega gallade in his place.

"Impressive, but insufficient. You have stopped nothing, you have merely picked your gravesite" she yelled.

"If that is my fate so be it" Malcolm conceded.

Lana scowled and said "This whole time, right beneath your school , he was right about you, such arrogance"

Malcolm said nothing

Lana then dropped a small illusion around her neck, revealing a silver collar with a latiasite in the center.

Lana glowed bright red, when the light faded her appearance had altered dramatically.

The red parts of her body had changed to purple. Horns had grown from the side of her head and runned along her jaw. She had no wings on her back, similar but larger wings were now attached to her lower arms. Triangle shapes now marked the forward point of her wings instead of her chest.

The newly evolved Latias smiled and said "Your mega evolution is nothing compared to mine, no one will save you. You cannot hope to survive"

 **Author's note- cliffhanger time :)**

 **Thank you guys so much for making this story as popular as it is, you all are amazing.**

 **Leave a review or follow the story, I would really appreciate it.**

 **See ya all next chapter** ️


	25. Chapter 25

Chapter 25

3rd person POV

The stadium was clear, only a green Latios remained to fight the corrupted Rayquaza.

"The lord of the skies, how did they catch you in the first place" Connor thought as he dodged another dragon pulse.

This was the first time in years he'd been at his full combat speed. Everything was moving in slow motion to him.

He then began to blast it with luster plurge, he just hoped it would work.

Unbeknownst to most, luster plurge was the most versatile move in the world. Connor had created multiple variations of the move himself. It could be a beam, focused into shockwaves or even ropes of energy to ensnare foes. It's most important trait however was the one Connor was trying right had not hunted the Lati just because they were rare. It was because luster plurge is able to instantly purify shadow Pokémon. A trait that Cipher would do anything to snuff out.

Connor kept up the blasts, but it had no effect, he would need to knock Rayquaza out to purify it.

Rayquaza roared in frustration and began to shoot hyper beams in every direction.

One beam shot past Connor, he turned and went wide eyed. The beam found its target, a massive gash was torn into a high rise apartment building began to tilt, then with a horrid screech of snapping metal it collapsed.

Connor saw red, hundreds of people had just been killed, he had to end this NOW.

He rushed towards Rayquaza, the black dragon couldn't have hope to see this coming.

"I'm sorry, but I can't let you hurt anyone else" he thought as he turned his hand intangible.

Connor thrusted his phased hand into the beast's head then un phased it. Crushing Rayquaza's brain and killing it instantly.

The beast went limp and fell to the ground, causing a dust cloud as it landed.

It was over, Cipher's ultimate weapon was dead.

* * *

Gregavich's POV

My jaw dropped, the pinnacle of our work was gone. The skydancer had ruined everything in a matter of seconds. It would take years to replace XD-2. The master would have my head.

I turned to the staff, they were completely still, awestruck by what had just transpired.

"Are we blind, prepare to evacuate, delete all server data, MOVE" I yelled.

I was no fan of retreating, but we needed to cut our losses and save what we could.

I picked up my headphones and radioed Lana.

It was time to leave.

* * *

Lana's POV

I screamed as the gallade's blade slashed my side, this was not going well. He was far more formidable than I imagined.

I blasted him back with mist ball, I could feel the blood dripping down my side.

"Lana, XD-2 is dead, we need to retreat" the doctor yelled into my earpiece.

As he said this Malcom slashed me again, slicing my eyelid. Luckily I had closed my eye, but I could feel more blood dripping down my face. I fell to the ground exhausted.

"Surrender" he demanded in between pants.

I began to shake, i couldn't give up. The orb was right there.

"I REFUSE TO LOSE" I yelled.

I casted an illusion, making mirror Images of myself and sending them towards Malcolm.

It was time to end this.

* * *

Alex's POV

We entered the vault via a secure elevator that was hidden in Malcolm's office.

The door opened and my jaw promptly hit the floor.

The professor was fighting Lana, at least I thought he was. The battle was happening so fast that it only appeared as 2 blurs were clashing back and forth.

Then one of the blurs seemed to turn and charge at us. We all were petrified, we couldn't have hoped to block or dodge something so fast.

I closed my eyes, expecting a killing blow. This was it, all we had done was for nothing.

The hit never came, I opened my eyes and saw a gallade in between us and a Latias-like Pokémon.

A pit grew in my stomach, the professor had been impaled by Lana. His eyes were glassed over, he wasn't breathing.

Lana pulled out her claw and the professor fell to the floor, dead.

"Such foolishness" Lana scoffed.

I snapped, something within me surged through my body and shifted me instantly.

I blacked out after that.

* * *

3rd person POV

Alex began to glow blue, his lucario form was projecting an aura so powerful that you could see it with the naked eye.

The others simply stood there in shock.

Alex's eyes were pure blue, no pupils just a glowing blue.

He put his hands together and gathered energy for what looked like a gain aura sphere.

Lana floated back cautiously, even she was stunned by this new power.

Alex unleashed a blast of aura, it wasn't a sphere, it was a massive beam of pure energy.

Lana was blasted back so far back she ended up smashed into the wall on the other side of the room,forming a small crater in the stone wall.

Alex began walking towards her, he seemed completely devoid of emotion.

Terror was apparent on Lana's face, she made a lightning fast dash towards the massive gen on a pedestal.

She grabbed it and vanished, just before Alex delivered a glowing punch into the air where she would have been.

The aura around him dissolved and he collapsed, shifting back as he hit the ground.

The other shifters ran towards Alex, worried about their friend.

"He's just unconscious" Dana said.

Everyone breathed a sigh of relief. Alex was going to be fine.

Then reality hit them like a brick wall, the professor was dead.

"Malcolm" A green latios asked as he entered the room.

No one said anything

His eyes went blank. He already had figured out what happened even before he saw Malcolm's body.

He flew up to his foster father's body and promptly fell to the ground, so shocked he couldn't even levitate. He then began to weep, too broken to do anything else.

Professor Andrew Malcolm, their teacher, protector and friend, was dead.

 **Author's note- this is not a joke or a plot twist I'll simply undo, Malcolm made his choice and died so his students could live.**

 **Yes Connor is THAT powerful, but as I said he never goes all out due to how much it scares him. To give you some perspective he was moving as fast as quicksilver's famous kitchen scene in xmen days of future past.**

 **I'm not sure if this chapter qualifies as M rated, tell me if it does.**

 **Leave a review and follow this story**

 **See ya next chapter.**


	26. Chapter 26

Chapter 26

3rd person POV

The rain was heavy, it was strangely appropriate for the event today.

As the downpour continued a parade of black umbrellas gathered around a large tent, a closed casket was carried into the center of the area where a hole was prepared.

Alex, Cassie, Jake and Charlie were confined to the back row of chairs, the front row was exclusively for direct family.

As the obituary was read Alex was a statue, he was simply not there. His eyes were blank and cold.

Cassie was similarly still, but she noticed a single empty chair in front of her. She knew that the chair's occupant was here, he simply was too ashamed to be visibly present.

Hovering above the funeral an invisible object was transfixed on the ceremony. Despite living among them for years human customs were mostly alien to him.

Why go through so much trouble to bury a box with the body in it. Malcolm wasn't there, merely a cold shell where he used to be. This was simply dragging out the time to grive, the box only served to remind Connor of his failure to help his foster father.

Once the processions were over Connor shot up into the clouds. It was time to go home, the egg was going to hatch at anytime now.

He wouldn't miss the hatching of his first child for anything.

* * *

The tension in the master's throne room was higher than it had ever been. Every Admin was gathered at a tabel with black chairs, the master's throne was at the head, with a slightly more ornate black chair at its right side.

This was the first full council meeting in years, 10 years in fact. The room was locked on all sides, except for the biggest door at the end of the room. Along the wall the torches were burning brighter than usual, the crackling of the flames only increased the dread of the meeting.

5 people sat around the table. None of them seemed confident that the master would be ameanible to reason

Nikolai, a master assassin who trained Ethan's team. His armored bodysuit covered numerous scars from his missions. He had his infamous helmet removed revealing a scar across his left eye. He was the only admin who was not a shifter

Victor was a brute, both in physical stature and personality. He was a machamp shifter, he loved practicing with his 4 armed shift form and had mastered 20 disciplines of martial arts.

Sophia was the oddball of the group. As a ninetails shifter she was more than capable of fighting and doing missions but had decided to be the master's public figurehead. She maintained control over Silph-co and all other companies that backed cipher. She excelled at keeping these publicly favored companies in her pocket.

Gregavich was swiping picture after picture on his tablet, he always tended to get lost in his work when he was nervous. He was studying photos on ancient tablets and books. Trying to find a replacement for XD-2.

Lana was to the right of the master's throne. She had worked nearly her whole life to sit in this chair, and she would fight to keep it.

"Nervous Lana" Victor taunted.

"You're one to talk, what have you done for our cause recently" she snapped back.

"Enough the both of you, let the master be the first to lay down judgment" Sophia barked.

"I'm just saying that…." Victor was cut off as the door opened.

Everyone at the table stood up and kneeled as the master walked past. The banging of his boots was the only sound in the room.

He was flanked by 4 Bisharps, two of which had blue armor instead of red. While the red Bisharps rotated between admins the blue ones were always at the master's side. They were faster, tougher and stronger due to a mix of brutal training and shadow energy treatments. These treatments were small and precise, they had only enough energy to use weaker shadow moves and slightly enhanced physical abilities.

As the master reached his throne he looked to Victor and said "Victor, do you find such malignance necessary"

With a motion of his hand the admins stood up and took a seat.

"Today we have suffered a grievous defeat" the master sighed.

No one said anything.

"However none of you are to blame for this, once again we find ourselves caught off guard by an uncontrollable variable" he admitted.

"But master, Lana should have killed the skydancer when she had the chance, this is her fault in the end" Victor said. His tone reeked of disdain.

Everyone went wide eyed, Victor had just told the master that he his judgement was off.

The master looked at Victor"maybe so Victor, but I don't see you doing anything useful recently. You are in no position to judge my prefect" he scolded in an icy tone.

The master then shook his head. "We need to take a step back, the MRPA is going to be keeping a watchful eye on any suspicious activity after the PWT was openly attacked".

"Dr Gregavich, see what you can learn about the adamant orb, you should also keep looking for a replacement for XD-2" he ordered.

He then turned to Victor and said "Victor, I'm sending you to our base in the whirl islands, see to it that the research there is on schedule"

Victor nodded

"Sophia, return to Silph-co. The chairmen continues to prove loyal, ensure that the board is kept in line" he requested.

"Yes master Ardos" she responded.

"Nikolai, I have an assignment that will require Granite team, make sure they are trained and ready" he continued.

Nikolai frowned but kept his opinion to himself.

Finally he looked at Lana and said "Lana I need you here, your knowledge of lati abilities will be most beneficial for developing more countermeasures for their abilities"

Then he stood up and spoke to the whole table. "We have made great progress in the past year, do not let XD-2's death derail it".

The master then stood up and left, his Bisharps close behind. The MRPA may have won this round, but the war would be his.


	27. Chapter 27

Chapter 27

Author's note- It's been almost 2 years since the events of chapter 26

Dana's POV

I was greeted by a massive security detail the second I left the plane. My parents were always thorough.

I never told the others but my parents were some of the richest people in the world. They owned both the poketech company and most of the pokeball production around the world. Anyone in their right mind would ask why I didn't run back to them once I was safe.

Simple, they are the worst patents ever. They are always gone, never listened to me, and act like I'm a defenseless little girl. Despite all that they still wanted custody of me,I'm 17 not a baby.

I got kidnapped because of my parents neglect. They sent me off to boarding school and I got scooped up by Cipher.

As I entered the mansion I was greeted by my Mom and Dad along with the entire staff. They ran up to me and gave me a hug.

"I was so worried about you" my mom exclaimed.

"Don't worry, you'll never have to see those MRPA thugs again" my father said proudly.

"I need to go to my room" I requested.

"Ok, Jackson get her bag" she ordered.

My personal butler ran up and grabbed the bag. I simply followed him to my room as my parents went their separate ways.

I entered my room and Jackson set the bag on my bed. The room was clean and cold, just like I left it.

"Anything else miss Lance" he asked.

"No Jackson, that will be all" I said with a sigh.

"Very well then, ring the bell if you need me" he said as he opened the door.

Before he left he turned and spoke in a hushed voice " I know the legal battle for your custody was hard, and I know your not happy here, but if I can do anything to help I will" he offered.

I gave a small smile as he closed the door and left me alone.

I opened my bag and began to unpack, making sure to organize things properly so the butlers wouldn't go through my closet. I couldn't afford for my parents to find my mega stone. It was my most prized possession, along with the only thing I had to remember Veilstone.

My parents had no ill harbor against me being a shifter, but I was strictly forbidden from using my powers in public. They said it was to protect me from unwanted attention. In reality however, they simply wanted me to hide it due to it not being a good image of a perfect family.

Where I inherited the gene was a mystery, but I had a pretty good guess. My parents never talked about my Father's Father. He was an outcast from my family, never invited to family gatherings. He was most likely where my father got the gene but skipped a generation.

I finished in packing and looked at my mega stone. I found it at a jewelry store and bought it for cheap. The manager clearly didn't know what it was. After I bought it, I smashed the necklace it was in and fitted it into a small bracelet.

"It nice to have something to hold onto the past isn't it" a voice said from behind me.

I turned around and saw nothing. I must have been hearing things.

"You're not hearing things" the voice said.

Out of nowhere the mystery shifter from Veilstone appeared in front of me. His sunglasses were gone revealing his blood red eyes.

"How did you get in here" I asked.

"I can turn invisible and phase through walls, do the math" he joked.

"I'm surprised you came to see me, how are the others doing" I asked.

"Alex is in college in Jhoto, Cassie and Jake went back to Unova with their mom and Charlie is still with the MRPA" he explained.

"They all went their separate ways" I said, surprised by the news.

"Not by choice, Alex, Jake and Cassie's parents demanded them back, Charlie has nowhere to go so the MRPA made him a special agent" he admitted.

I heard voices coming up the hall.

He gave a sigh and said "I'll check in again if you want"

"Sure, drop in when you can" I requested.

He nodded and dropped his illusion, soon the green latios disappeared and I was left alone again.

I just hoped the others hadn't forgotten me.

Alex's POV

* * *

I went into the barber shop and rang the bell. Soon enough Mike came out of the back.

"Hey Alex, long time no see" he said happily.

"Two years are way too long" I replied as I took of my hat revealing my natural hair.

"Back form that snotty school in Sinnoh" he said as he sat me down and put a towel around my body.

"Yea" I replied in a hollow voice.

As he cut my hair we chatted on and on. I mainly asked questions.

"Why'd you leave" he inquired as he returned with my black hair dye.

"Got picked on for being a shifter" I lied.

"Really, at least you got out before that black dragon showed up" he remarked as he shook the can.

I closed my eyes waiting for the spray but it never came.

"Whoops, I just got my shipment for the month, guess I should've checked my stock better" he said as he tossed the can.

"Wait what, you can't be serious" I asked as he shook his head.

"Sorry man, it's just a month though" he said reassuringly.

I sighed and said "okay, how much do I owe ya"

"On the house man, have a great day" he said as he walked back to the store room.

I simply put my cap back on and left. Doing my best to hide the wisps of red hair around my forehead. Hopefully people would think I just dyed it a new color, everyone though my natural hair color was black. I hoped I could keep it that way.

Little did I know what awaited me when I got home.

 **Author's note- sorry about the long wait, life has been crazy for me.**

 **Yes Alex has red hair, fans of my favorite Pokémon game will know who is father is, and what complications that has for the story.**

 **Leave a review, it always makes my day**.


	28. Chapter 28

Chapter 28

3rd person POV

"Lisa, where is he" Connor asked impatiently.

"Just playing with his friends" she replied.

"I'll go check on him" Connor said as he zoomed off.

Lisa frowned as her mate left, he was just too overprotective sometimes. The hatchling was already 2 years old, and skydancers matured faster that most lati. He was already the equivalent of a human 6 year old, he wasn't completely helpless.

Zander was an almost mirror reflection of his father. He had the same distinct green feathers and incredible flying skills. After he hatched his father refused to let him even get close to leaving the sanctuary.

While he didn't seem to care, Lisa was worried that her son simply needed more social time. He needed friends like any young lati.

Eventually Connor returned with Zander beside him. The hatchling looked saddened by his father's return.

"Why can I no play" Zander asked.

"Because you're mother and I love you so much and want you to be safe, now go lay down in our grove, I'll be there soon" Connor asked

Zander gave a smile and did as his father asked, leaving Connor and Lisa alone.

"You can't isolate him like this forever" Lisa said.

"I know, but I want him to be monitored by you or Norin constantly" Connor said vaguely.

"But why, I keep tabs on him but he needs to be around others" she pleaded.

"I know, I just see too much of my sister in him" Connor sighed.

"What do you see" Lana asked.

"I see a young lati who maturing far too fast for his age, who has too many skills for his age and seems to like those skills. I can't lose him, I just can't risk it" Connor explained.

Lisa noticed a small tear in his eye, she didn't need to be psychic to feel his sorrow. The blankness in his eyes, his persona of strength was gone, only dread and sadness in its place.

Lana nuzzled her mate and motioned for him to follow. They went to their grove and called it a night.

* * *

3rd person POV

"I hate Mondays" Jake groaned as they left class.

"You can say that again" Cassie seconded.

As they were walking to their next class Cassie's purple hair started to get frizzy. She quickly brushed it down and pulled her hoodie over her head.

They entered the lecture hall and sat down. Collage history was always Jake and Cassie's favorite subject.

The teacher walked in and said "good morning class, turn to page 57 in you textbook, we will be going over early Jhoto history and mythology.

"You ok?" Jake asked Cassie, she was shaking.

"Ms. Simmons, no hoods inside please" the teacher said.

Cassie shook her head.

"Please don't make me stop class" the teacher requested.

Before Cassie could respond a boy in a brown t-shirt grabbed Cassie's hood and pulled it down, revealing her purple hair.

Everyone looked as Cassie like she had two heads. She quickly began to cry and ran out of the room. Jake tried to grab her arm but received a static shock.

"Mr Simmons, you are excused, make sure she's ok" the teacher said.

Jake nodded and ran after her. He looked all over the campus and eventually found her sitting on a bench, alone and crying.

"Cass don't worry, I'll be sure to find somewhere else to sit" Jake said.

"Everyone saw my hair, I'm a freak and everyone knows it" she sobbed.

Jake sat down and pulled her into a hug, allowing her to cry into his shoulder.

"You're not a freak, you're my sister and my best friend, I've always had your back haven't I" he said in a calm voice.

Cassie managed to stop crying, she broke from the hug and wiped her nose. She looked at her brother with renewed vigor and nodded.

"Let's go back to class" Cassie said.

As Jake and Cassie entered the lecture hall they noticed class was still in session.

"Ah Mr. and Ms. Simmons, we just started talking about the burned tower, please have a seat" the teacher said.

Cassie frowned as she opened her book. Why did that name sound familiar.

"The burned tower was once just as tall as the tin tower, however a fire broke out and reduced most of the tower to ash. Three nameless Pokémon were killed" the teacher explained.

As everyone took notes the teacher continued saying "Once the fire was extinguished by rain, legend says the guardian of the skies Ho-oh descended and resurrected the Pokémon. Those Pokémon became the first Entei,Raikou and Suicune. Despite the many signs that point to this story being true, no one has ever provided proof that the legendary beasts exist"

Jake gave a small chuckle, he and Cassie were living proof that the beasts existed, heck they had met the real deal.

"Is there something you wish to share, mr Simmons" the teacher said.

Jake went wide eyed, he had to think of an explanation that wouldn't expose him and his sister.

"Well how do we know it's mythical, everyone watching the PWT a few years back saw a living breathing Rayquaza" Jake said quickly.

"That was a publicity stunt by the Pwt, the building collapses were caused by an earthquake, there was no real deaths there" the brown shirted boy said.

Cassie turned around and grabbed the boy by the collar. Her body was giving off small sparks.

"Cassie, cool it" Jake yelled.

"You don't dare speak like that, you have no idea how many lives were lost on that day, SHUT UP OR ILL TEAR YOUR THROAT OUT" she screamed.

Cassie's eyes were blood red, Jake could see the sparks on her body getting stronger, he had to do something before Cassie hurt someone or shifted in front of everyone.

He was too late, Cassie threw the boy across the room and fell on all fours, shifting into a Raikou with a hellish roar.

Jake shook his head, he didn't have a choice. He quickly shifted as well, he had to stop her.

Cassie began to charge at the boy only to be blasted through a wall by a massive kanji of fire.

Everyone looked over to see an Entei charging after the Raikou.

Jake tackled Cassie as she stood up. He shot her with a sacred fire point blank, ending the fight in seconds.

Jake shifted back and ran to his locker, he needed to find some clothes. He managed to put on his gym outfit and get back with Cassie's just as he heard sirens outside.

As Cassie woke up Jake tossed her an outfit and said "get dressed we gotta go"

Cassie nodded and put out their outfit. They then ran outside only to surrounded by armed MRPA agents with tranquilizer guns. They immediately raised their hands, they had to come quietly.

"Targets secured, get commander Daniels" one of them said.

Cassie and Jake were ushered to a roped of area off the parking lot with shift collars on their necks. Soon a chopper descended, the doors opened and an all too familiar face excited.

"Well this is quite a mess you two" Charlie said.


	29. Chapter 29

Alex's POV

"What a day" I scoffed as I took off my hat.

"Alex, we have a visitor. Come here please" my mom called from the kitchen.

I entered the room and my face twisted into a scowl. Standing next to my mom was a man in a black business suit. His blue eyes were kind, but I was still on edge. His blood red hair was the exact same color as mine. His smile did nothing to calm my nerves.

"Hey Alex" my father said calmly.

"You've got some nerve to show up now" I said.

"Alex please give your a father a chance" my mom asked.

I briefly went silent and checked my father's aura, he was genuinely trying to be nice, but he was nervous about something else that I couldn't read.

"Why are you here" I asked cautiously.

"I just want to see my son" he explained.

"Yea right, your about 10 years too late for me to care" I said as I walked away.

I sat down and turned on the tv in my room. The news was going as usual when the anchor paused. He held his finger to his earpiece and went quiet, his face went from happy to shocked in seconds.

"Apologizes for the delay ladies and gentlemen, but a terrible tragedy has just occurred on the island of Altomare" he announced.

I went wide eyed, Connor said that's where he was living now.

"We now take you like on the scene via our sister station's helicopter" he said as the camera cut to an overhead shot of the island.

A massive part of the city was on fire, the rest looked like an hurricane had come though. Houses and buildings were in shambles, but oddly the devastation was in a straight line leading towards the exact center of the island.

I knew Cipher was behind this, Cassie told us the Lati sanctuary was in a garden near the city center.

I ripped my phone from my pocket and dialed a number I had made sure my mother didn't know about.

"Hello, this is special agent Daniels" Charlie asked in a rushed voice.

"Charlie, is Connor ok what about Altomare" I asked is rushed voice.

"Cool it Alex,MRPA is headed that way, I'll call you when I know ok" he said, immediately hanging up the phone.

I simply sat on the couch and waited for the call. I just hoped Connor was ok.

* * *

3rd person POV

"Into the tunnels go!" The elder yelled.

"60% of the herd is accounted for " Connor said as the single file line of Lati continued into the hole, diving one by one into the underwater caves hidden beneath the garden.

Females and hatchlings were first, along with a select group of males. 8 of the strongest Current Chasers and the only 2 Leviathans in the herd.

Lisa and Zander were right at Connor's side, unwilling to leave him.

"Lisa, you and Zander have to go NOW" he barked.

"I'm not leaving you, never" she responded firmly.

"This isn't up for discussion, you need to keep our son safe, Cipher can't know about him" Connor said.

Lisa looked to her son then back to Connor. Her eyes were growing wet with tears. She steeled her resolve and dove into the tunnels.

Just then an explosion shook the entire ground. A massive hole was blown open in the wall, despelling the psychic barrier around the garden.

Norin and 3 Ferals flew in. They were covered in cuts and bruises.

"We're completely surrounded, most of the shadow Pokémon are down for the count but there's just too many soldiers" one of the Ferals said.

"Elder, you need to go, we'll hold the line" Norin said.

"Ok, if the two of you survive, head to the rally point we discussed" he said. He motioned for the Ferals to follow and dove into the tunnel.

Connor closed his eyes and used his psychic energy to close the door. They were on their own now.

"How heroic, the master will still be satisfied with you twos carcasses" a voice ringed out from the hole in the wall.

He saw a glowing ball of light heading towards him, he put up a reflect and vibrated to full combat speed.

The orb missed him however and hit Norin, the current chaser could never have hoped to dodge something so fast.

Connor could only watch as the attack blew a hole clean through his cousin's belly. His internal organs were shredded.

Norin coughed up blood, then his psychic energy dissolved and the young Latios fell to the ground. His eyes were glossed over and his blood pooled around his corpse.

Norin, Connor's best friend, last living blood relative and the closest thing he had to a brother, was dead.

Dr Gregavich entered the garden with the 20 remaining soldiers coming in from all sides. Connor was on the ground weeping next to his cousin's body as the soldiers surrounded him and leveled their rifles..

"So another of you family dies by my hand, oh well, your turn" he joked.

Connor let out a feral scream of agony, releasing a shockwave of psychic energy so powerful that all the soldiers in the vicinity had their brain and nervous system fried from the inside out. The soldiers fell to the ground, foaming at the mouth and contorting their muscles.

Gregavich's shifter DNA spared him the same fate. However despite all his power and training he was legitimately intimidated.

Connor closed his eyes and took a breath, then he floated up off the ground and stared the doctor down.

"No more hiding, no more holding back, I'm going to tear you limb from limb" Connor growled, the bloodlust in his voice unmistakable.

Gregavich attempted to teleport but he found he couldn't, he looked far more scared than before.

"Psychic impedance field, an experienced user can make one to stop teleporting, you're not getting away this time"Connor said harshly.

Gregavich shifted and flew straight towards Connor. He surrounded himself with a ball of light, charging into to Connor at full speed. He hit Connor head on, but the skydancer blocked the attack with a reflect, somewhat effortlessly.

Gregavich received a luster plurge at point blank range, he was hit so hard that the attack created a small crater in the ground.

Gregavich applied a barrier around him, hoping the psychic bubble would buy him enough time to use recover and heal himself.

Gregavich closed his eyes, a green light enveloped his body as Connor began to pound on the shield with dragon claw.

Gregavich was only about halfway healed, but he could feel the barrier weakening with every slash of the latios's claws, he wasn't gaining ground, time to show his hand.

Gregavich closed his eyes and focused on the stone in his shift suit. He felt his body begin to morph, his muscles fading into a thinner sleeker body, now solely depending on psychic energy.

The newly evolved mega mewtwo Y released a shock wave, knock the latios back.

"Your finished" he yelled.

Gregavich unleashed everything, blasting the latios with attack after attack. Showers of psychic blasts and thunderbolts rained down across the garden. Even at full speed Connor was struggling to dodge the onslaught.

Connor shot a luster plurge only for the beam to collide with a superpowered ice beam.

The beams were at a standstill, but the ice beam eventually won out and hit Connor dead on. The ice froze his wings solid, he fell to the ground like a brick.

"You've lost" Gregovich gloated as he charged up a final ice beam.

The latios smirked, he didn't seem remotely concerned.

"Is that the best you can do?" he scoffed.

Gregavich went wide eyed, only now noticing a stone around Connor's neck.

The ice shattered as Connor surrounded himself with a massive orb of psychic energy. His mere presence releasing shockwaves powerful enough to blow Gregavich back.

"FOR MY PARENTS" Connor yelled

The light around Connor grew to a blinding intensity. When Gregavich could see again a dark green mega latios was inside a pillar of light. The light could be seen from miles around the island.

Gregavich casted a barrier, but the mega evolved latios was giving of enough raw power that his simple being there was causing cracks to form throughout Gregavich's strongest shield.

Connor unleashed a luster plurge that was not its usual purple but a white beam of pure destruction.

Gregavich could only scream as his shield shattered, the beam hit him and he was completely vaporized. Only ashes and a megastone remained.

Connor's mega form dissolved and he fell to the ground, completely spent.

He passed out, knowing only that Norin was dead, and the doctor along with him.

 **Well, that escalated quickly, fans of the web show death battle will know where the insperation of a transformation causing a beam of light to shoot up into the sky came from.**

 **As you know its been a while but I hope to update more offen.**

 **This story will be M rated from now on, only dur to violence and gore occasionally.**

 **leave a review :)**


	30. Chapter 30

Chapter 30

* * *

 **Author's Note- it's been 2 weeks since the events of chapter 29**

3rd person POV

"YOU LET THIS HAPPEN!" The master yelled, slamming his fist on the table and causing a huge crack to appear in the black granite.

"Master, what was I supposed to do against such raw power" Victor responded nervously.

"You were supposed to not let him kill the doctor, the power you described is impossible" the master reprimanded.

"But you cannot deny that" Victor tried to explain but the master raised his hand and a shadowy aura appeared around Victor.

Several black misty arms appeared from the floor and pulled Victor to his knees. He was slowly suffocating from the arm around his neck,

"Master, I have something to legitimize Victor's story. Please release him" Nikolai asked in a worried tone.

Ardos scowled for a minute but lowered his arm and the mist around Victor's neck dissolved.

Victor coughed and began sucking air due to the stranglehold.

"Show me" the master demanded quietly.

Nikolai opened his laptop and turned it towards the master. It showed the view of a soldier's helmet camera just before the doctor's death.

"A psychic wave killed the soldiers but his camera kept filming" Nikolai explained.

It showed the doctor fighting in his mega form, freezing the skydancer to the ground only for him to bust the ice and summon a glowing ball of light around him. There was a bright flash and the camera feed went dead.

Shadows swirled around the master, he was seething with rage.

"Leave, I wish to speak to Lana privately" he said through clenching teeth.

Every admin ran out of the room, leaving Lana and the master alone.

Lana bowed her head "Master Ardos I sincerely apologize for.."

"Stop, the room is secure and HE wishes to speak to you personally Ardos said calmly.

Ardos removed his black glasses and his blue eyes turned red. No pupils were present, simply glowing red orbs.

The room became colder, the air was stale. Torches on the walls dimmed, almost as if the presence of this new entity inside Ardos's body sucked all life and joy out of the room.

"We HaVe sUFFered a GrAve lost LAnA, but wE must PreSs OnWARD" a distorted voice said. This voice was a mix of Ardos's voice and a deeper, far more malicious one.

"Yes my lord" Lana said with a respectfully bowed head.

"Go tO tHe TRIton sTation aNd OVersee the DoCtor'S work, and IF YOu see YoUR BroTHER, KILL HiM" the ominous voice barked.

"Yes my lord" Lana responded.

"RIse mY DisciPLe, and AchiEVe YOur gOal in MY NamE" the voice said before going silent. The torches burned brighter and the air returned to its usual state.

Ardos's eyes returned to normal, his body went limp and almost fell out of his throne. He looked like a marionette who had just had its strings cut.

Ardos's shook his head and returned to his normal posture.

"You have your orders Lana" Ardos said bluntly, he stood up and left the room.

"And I will carry out those orders" Lana muttered to herself as she headed to the door.

* * *

Jake's POV

I walked up to Crawdaunt club in goldenrod city with a frown on my face. Why did the MRPA send me here on my first mission? All they told me was a critical field asset had been out of contact for 12 days, and needed to be checked on. I checked his listed apartment and all I could find was a receipt to this place. The apartment was cleanly furnished and the bed was the only messy thing in the place.

I was stopped by the bouncer at the door, annoying but to be fair I didn't exactly look like my true age of 24, stupid legendary DNA.

"Sorry kid, but your not fooling anyone" he said putting his hand on my chest to stop me.

"I'm a bit above your pay grade buddy" I said retrieving my MRPA badge.

"Yea, right" he joked as he looked over my badge. Soon he fell silent, he realized I was legit.

"I don't want to cause trouble, but I need to get through, one way,.. or another" I threatened falsely.

I summoned a small flame in my hand for effect, he handed me my badge and stepped aside.

I entered the bar and saw a table covered with bottles, enough alcohol to make 10 people drunk.

At the center of the tabel was an all too familiar teen with blond hair and red eyes. His illusion looked a little older than before but the red eyes were a dead giveaway.

"Connor?" I asked in disbelief as he slammed down another bottle.

He reached for another bottle but I stopped him.

"What, I payed for it" he said in a clear and focused voice.

"How" I asked in disbelief.

"MPRA gives me a living fund, and I don't use it for anything else since I hunt for my food" he explained.

"But how are you still conscious and why are you drinking" I pressed further.

"I thought it might dull my guilt a little, but my metabolism burns so fast, I can't get drunk" he admitted.

"Altomare wasn't your fault, you're herd survived because of you" I said trying to get through to him.

"Yea it was, my cousin is dead and a third of the herd along with him. All because I was too scared to use my power, too scared to fight back" he sobbed as tears filled his eyes.

"Come on, I'll take you home, get some sleep, then we can talk more, your too strong to give up like this" I said offering him a hand up.

He went silent for a moment he looked at my hand.

"Ok, but no rest, let go to HQ and get started.

I smiled and we left the bar. Maybe all hope wasn't lost.

We reached the forest and he dropped his illusion.

He looked at me and motioned to his back. He was practically begging to fly.

"I'll flameport there, get a headstart" I offered.

"You better be fast" he taunted.

With a smirk he took off at a blazing speed. He flew straight up and disappeared into the clouds.

"Show off" I muttered.

* * *

 **Thanks for the views, leave a review.**

 **I hope people still like this story….**


	31. Chapter 31

Chapter 31

Alex's POV

I sat in my room alone, watching TV. It was all I had to do right now.

Charlie called me back and explained everything he could. Connor's herd took a huge hit, but he had managed to kill the doctor, Cipher fled soon after.

I was relieved that Gregavich was dead, one less psychopath to worry about. I sadly knew that it was little more than a Pyrrhic victory, Altomare was gone, merely a pile of rubble where the city once stood. Even when the MPRA won Cipher was still on top.

Hope was all I had left, I was old enough to join the MRPA officially but my mother wouldn't have it. I just felt so useless.

There was a knock on my door, I opened it and came face to face with my father.

"What do you want" I asked.

"I just want to talk" he said cautiously.

I stared him down for a long time, his aura showed he was genuine. I sighed and allowed him in.

"I know you don't trust me, and I'll leave as soon as you let me say my peace" he offered.

He sat down on my bed next to me, being careful not to sit too close.

"I know I abandoned you, and I know you don't care about my explanation, but I want you to know I always loved you, no matter what I never stopped doing that." He reassured me.

"I might be to blame for you being a shifter, I'm aura sensitive after all. I can sense that there's something aura related that's bothering you as well" he asked.

"One time, during the Veilstone crisis, when the professor died, something happened" I said, forcing the words out.

"Describe it" he asked softly.

"That's the funny thing, I can't remember it. All I remember is seeing the professor dying then blacking out. Charlie told me that I did something crazy after that" I continued.

"Define crazy" he asked, he seemed very curious.

"Apparently, My eyes glowed a bluish white and my aura was visible to the naked eye. I blasted the Cipher agent with a massive beam then collapsed" I explained.

"I know what it was" he stated vaguely.

That caught my attention, I looked him straight in the eye and said "tell me"

"Ok, you know how every Pokémon has aura, that's how they take hits without much physical evidence of damage and when it's depleted, they are prone to real injuries?" He explained.

"Yeah" I said, still confused.

He smiled and said "What you described sounds like a rare phenomenon where a powerful aura user can tap into a deeper well of aura that is hidden within them and supercharge their outer defenses, simultaneously boosting their attacking capabilities"

"Wait, why haven't I ever heard of such a thing" I asked.

He looked away and said"It's ludicrously rare, it's the same odds of having three triplets being shifters and their shift forms are shiny" he explained before getting back to what we started talking about.

"Anyway, I know you hate me, heck most of the world hates me and my family, so I understand why you hide your red hair, I just hope someday you'll forgive me" he begged

I turned away from him

"Nonetheless, I love you and I've said my peace, I'll be leaving now" he sighed.

With that he left, leaving me alone to mull over what he said.

I heard him say goodbye to my mother followed by a shutting door.

My mother came up with a small envelope in her hand, I could feel the hesitation within her.

She opened the package and retrieved a note, she handed it and the package to me "pack your things, I've decided to let you make the call" she conceded.

She didn't say anything else, she just closed the door. Ilooked over the note, it was short and to the point.

Welcome to the MRPA

Director Michael.

I then looked at the badge and gasped, I assumed I would have to start at the beginning, but the badge and its sleeve made my position very clear.

MRPA

Special Agent

Alex Mason

* * *

3rd person POV

Connor entered director Michael's office silently, he took a seat in front of the desk.

Green irises met red as they stared each other down.

"Good to have you back, you've done nothing wrong so relax" he reassured him.

"Cut to the chase, you want something from me so spit it out" Connor said sharply, he had a pretty good idea what this was about.

"Fine, where is your herd hiding now" Michael asked calmly.

"I can't tell you that" Connor stated, his tone made it sound like it was a fact.

"Please, we just need to know so we can send additional protection for them" Michael explained.

"I'm not trusting you or anyone else with the survival of my species" Connor stated firmly.

"Fine, but I hope you'll reconsider" Michael said.

Connor shook his head and left.

Michael picked up the phone and dialed Jake.

"Report" Michael requested.

"I'm in route, Cassie says she has some good news" Jake said.

Michael smiled"Good, hopefully this blacksite helps us find the new factory"

"I'll report as soon as it's secure" Jake responded.

"Copy, that" Michael responded.

"Simmons out" Jake said as he cut the call.

* * *

Cassie' POV

I heard a whoosh behind me and summoned a ball of electricity, only to see my brother behind me, materializing out of a ball of fire.

"Jeez a little warning next time, I nearly zapped you" I said as he knelt down beside me.

We were watching the building from a distance. Thanks to our shift forms we could see for miles, I could find electricity anywhere and Jake could sense body heat through walls so that was one positive of our burden.

"So this is it" he asked.

"Yep, way too much electricity flowing through the building. Whatever Ciphers doing is in the safe" I confirmed.

"Let's go" Jake said.

I grabbed his arm and said "slow down, there's two problems"

"Ok, walk me through them" Jake asked impatiently.

"To the locals this is a bank, if we barge in their with our badges Cipher will just lock the safe and wipe all the data" she explained.

"So we just go in and blow the safe open?" Jake asked.

I shook my head "no good either, the employees who don't work for Cipher will trip the alarm and get the local police down here, then we'll have to explain ourselves to them or fight our way out against innocent people"

Jake bowed his head and asked "any bright ideas Cass"

"Just one" I responded.

3rd person POV

"We'll transfer the funds as soon as we can" the commanding officer said to the monitor.

"The triton station needs the fuel as soon as possible, get to it" Kallahan barked.

"Alola Petroleum sent half a shipment in good faith, and the rest will be paid by weeks end" the officer assured.

"I hope so commander, for your sake" Kallahan threatened, simultaneously cutting the call.

"Transfer the funds, come on people MOVE" he yelled.

As he said this the lights dimmed, then they went out entirely.

"What the…"

Before he could finish his question the safe door started glowing, a small red dot appeared in the center of the steel. It grew larger and larger before the door began to melt. There was an explosion and the room filled with smoke.

The commander felt something hit him in the chest, like a car had just ran him over

When the smoke cleared every soldier was out cold, the smoke wasn't enough to kill anyone but it definitely took the air out of the room long enough to make someone pass out.

As he looked up the Cipher commander came face to face with an Entei. The massive beast's hot breath hit his face, he thought this was it.

Soon the beast stepped off him and began to shrink, a boy in a black shirt and blue jeans with ghostly white hair was soon before him.

"Thank god for that new clothing treatment" Jake thought as he cuffed the commander. He didn't have to wear a shift suit under his clothes anymore since the MRPA made a device to treat clothes so they shifted with him and that was a relief.

Cassie walked in with sparks flying around her. She touched a console and zapped it to life. After retrieving a flash drive and plugging it in the data copying began.

Cassie looked over the files as they copied, this place was a goldmine of information.

"Jackpot" Jake exclaimed.

"That's an understatement" Cassie said, motioning to the monitor.

Jake looked at the screen and gasped "that's the new factory"

"Not only do we have the coordinates, but there's delivery schedules and a complete copy of the blueprints" Cassie explained.

"This is it Cassie, Cipher's last factory" Jake said in disbelief.

"Unfortunately this isn't their headquarters, apparently the top leadership is somewhere else" Cassie sighed.

Jake shook his head "Doesn't matter, if we take this factory, their shadow Pokémon program dies with the doctor"

"Let's get back to base" Cassie said.


	32. Chapter 32

Chapter 32

* * *

3rd person POV

"Ticket" the guard demanded.

Dana flashed her ticket and headed inside. Failing to repress a sigh.

It was her parent's annual new year's Banquet. Despite her protests she was forced to attend.

Despite the fact that her 20th birthday had already passed she was still prohibited from leaving home. Her parents believed she wasn't ready for such a big decision and need to take her time.

In other words she needed to come to a decision that her parents approved of.

She had gained a few inches in height along with growing out her blond hair. She looked quite a bit different from her days in Vielstone. Only her hot pink highlights seemed to stand out.

While it seemed like a simple hairstyle in reality it was the dead giveaway of her being a shifter. Most shifters tended to have a physical identification even in human form.

Hair was the usual, sometimes even patches of skin were different, it was unique from person to person,

In Dana's case some parts of her hair were hot pink, like a Medicham's headress shaped forehead. Never enough to be obvious but visible nonetheless.

She was handed a glass of champagne on her way to the dance floor. Dana gagged and poured it in the trash. Dana then saw a new face in the crowd. One that her parents guest list didn't mention.

He had jet black hair, with a green handkerchief in his tuxedo pocket. His eyes were a very strange bluish red and he seemed rather on edge.

Dana's curiosity piqued when she noticed he was heading towards the bar alone, while everyone else went to dance.

She followed him and quickly nudged on his mind with psychic. His head was fortified and she couldn't read him, that was a red flag.

It took a powerful psychic to block another one without trying, let alone an experienced one like Dana.

She sat down next to him, and immediately felt a presence in her mind.

"Perceptive as ever Dana, you've been practicing huh" Connor's voice said telepathically.

"Why are you here, how did you get in" Dana wispered, shocked by Connor's different human guise

"Made an illusion of a ticket, your parents are working with a Cipher admin, we believe they are going attack and take them hostage" Connor explained silently.

"Is everyone else here" she inquired psychically as well.

"The Simmons twins are on standby outside, Alex and Charlie are on the roof as we speak. We need you to find the admin then we'll take over" he said as he finished his whisky, his human illusion showing no signs of the drink he had just downed.

Dana nodded and headed to the dance floor. Before she could go more than 10 feet her valet grabbed her arm.

"Miss Reinhard, your mother requests your presence at her tabel" Derek stated firmly.

Dana sighed and followed him to where her parents were sitting. Beside her father was a woman in a blue suit, she had creamy blond hair and silver eyes.

"Dana, this is Sophia, she had an interesting opportunity for you" her father said proudly.

"Yes, there's an internship in Alola I think you're the perfect fit for" she exclaimed.

Dana could already tell this was the admin, she looked off and her voice seemed way too sincere.

"So, who do you represent" Dana asked, carefully avoiding eye contact.

"Oh, I work for a Pokémon care company based on Alola" she said quickly.

That was strike two, Dana could feel her lying from a mile away.

Dana decided to act.

"How's your associates at Cipher HQ doing?" She asked quickly.

"Their doing" Sophia covered her mouth instantly.

"Checkmate, Connor Now" Dana yelled.

Dana shifted, tearing out of her dress and tackling her parents out of the way.

Sophia didn't even have time to comprehend the situation as a green latios slammed into her, knocking her out of a chait and pinning her to the floor.

"Impressive coordination, but not accounted for" she remarked.

In an explosion of bluish white flames Connor was knocked across the room. A regal looking Ninetails jumped out of the flames. She was almost to the door but Connor rammed her again, pinning her against a wall.

Sophia squirmed as Connor's clawed arms restrained her. She unleashed a deadly stream of fire right in Connor's face, but the skydancer's thick draconian skin took the hit like she was blowing air at him.

"Drop Her" A familiar voice said.

A teen in black armor with pointed ears had a sword to a party guest's neck.

"Ethan" Connor said coldly.

"Let her go, or I'll slice this lady's throat" he threatened.

However as Ethan said this a Raikou and Entei bursted on the scene.

"You shouldn't make threats when your so clearly outnumbered" Jake snarled.

Cassie was growling like a rabid mightyana, the rage she felt at the mere sight of Ethan was unmistakable.

"Easy Cass" Jake advised.

Cassie closed her eyes then opened them, she was still angry, but definitely more focused.

"Granite team, requesting backup" Ethan whispered into his earpiece.

"Your team is indisposed" Alex's voice said in response

Ethan went wide eyed, he was on his own.

Ethan began to move his arm but Connor didn't allow it. He moved so fast the motion wasn't visible. Ethan was disarmed and restrained by Connor in less than a second.

Sophia had been grabbed by Dana, the ninetails knew fighting was hopeless at this point.

"Get a shift collar" Connor ordered as Alex entered the room with a squad of soldiers.

"You thugs, you'll be hearing from our lawyers" Dana's father said as he got up and dusted himself off.

"Agent Daniels, take them into custody as well" Connor said dismissively as he reapplied his human guise.

"WHAT" Dana's parents said in unison.

"Mr and Miss Reinhard you are under arrest for money laundering, pokemon abuse, multiple charges of fraud and conspiracy with a known agent of Cipher" Charlie said as he cuffed them.

As they were taken away Dana went to the restroom and got dressed.

When she returned her parents were being shoved into a van. Alex came up and put his hand on her shoulder.

"I'm sorry Dana" he apologized.

"It's ok, they are getting what they deserve" she conceded.

"By the way, I hear your birthday was a few days ago and I got you a present" he said as he handed her a box.

Dana gave Alex a smile and opened the gift. Inside was a pair of earrings.

"Thanks Alex" she said.

"Not only that but I've got one more thing for you" he said with a devious smirk.

"What's that" Dana asked.

Alex handed her a badge and said "your 20, and with your parents in custody your free to start living your life, wanna join us" he offered.

Dana looked at he badge and thought it over. She nodded and shook his hand.

"Welcome to the MRPA" Alex said proudly.

* * *

2 days later….

The mood in the command center was tense. Michael pressed a button on the center most console and the monitors showed a readout of the Triton Station.

"This is Cipher's final factory, and a heavily guarded one at that" Michael explained.

The underwater facility was massive, it housed multiple submarine bays and explosive harpoon launchers to ward off any attacks.

"Michael, why not just have your lugia help us again" Charlie asked.

"No go, they'll be more than ready for him with those harpoons, we need a stealth option" he explained.

"Why not just drop depth charges and sink the place" Alex chimed in.

"I considered that, but they most likely have countermeasures, more importantly though this place must have information regarding Cipher's HQ" Michael admitted.

"So how do we get in" Alex asked.

"Give me some time, we have to have a concrete plan, I need a week at most" Michael requested.

"I need to check on my herd" Connor said.

Everyone started to walk away but an alarm went off. Every shifter in the room covered their sensitive ears.

"Warning, unauthorized breach in airspace multiple bogies inbound" The lead air traffic controller yelled over the intercom.

Then a massive boom shook the room, followed by four more explosive sounds.

"WARNING, perimeter breached, air defenses compromised, security alert in cell block" the base AI announced.

Michael looked around, everyone was awestruck. Cipher had found them and they were coming.

"Are we deaf, to your stations, get our birds in the air MOVE" he barked.

"Cassie, Jake, Dana secure the cell block" Alex ordered.

The Simmons twins nodded and ran out of the command center.

"Connor, get airborne and provide support to our choppers, No planes get anywhere near here" Michael said pointing to the hanger.

Connor nodded and vanished from view.

Michael pointed to Alex and Charlie and said "Simmons,Mason on me"

The two shifters ran after him as Michael entered his office.

He pushed over a photo of a Jolteon, a elevator appeared out of the floor.

"No matter what, no one gets through here, understand" he asked.

Both shifters nodded. Michael put the photo back up and the elevator sunk back into the floor.

The director ran out of the room, leaving Charlie and Alex as the last line of defense.

The two then noticed a blade punch through the ceiling. Charlie and Alex shifted, their new mega stones ready

Ethan and his team fell through the opening in the roof. The 5 soldiers in black armor were already prepared to fight.. Sandman's hands became covered in scales and grew garchomp hand blades on the fingers. Truck's steelix DNA took over his body and made his skin into artificial titanium. Grinch and frost surrounded themselves with an aura of electricity and ice respectively.

Ethan drew his sword, it was sparking with purple energy. He pointed the blade at his opponents and said "all according to plan, this ends NOW"

 **Another Clifhanger, god im horrible Muhahahaha**

 **leave a review for my longest chapter to date.**

 **Im considering taking a hiatus on this stoy and starting a mystery dungeon fic message me if anyone is interested in co-writing woth me...**


	33. Chapter 33

Chapter 33

* * *

Alex's POV

"You should've run while you had a chance" I threatened.

"Oh whatever, you're outnumbered and outmatched, this base will be destroyed and cipher will bring about the new world we desire" Ethan said proudly.

"You really think Cipher will make things better, your delusional, altomare is a pile of rubble and THAT'S what's best for the world" Charlie asked.

"A necessary sacrifice, the Lati there were too dangerous" Ethan rationalized.

I was about to respond but then I sensed something odd, Ethan's team was hesitating. Maybe they got the idea that Charlie was right.

"DIE" Ethan yelled as he ran towards Charlie.

Charlie reacted by grabbing Ethan's blade with a flaming hand. Ethan's blade melted like butter. He then was blasted back by a flare blitz.

Ethan turned to his team and yelled "Granite team, execute"

Sandman shook his head and looked away.

Ethan growled and disappeared in a purple flash.

I looked around, I could sense him teleporting around the room.

"AGHH" Charlie yelled.

I turned around, and gasped.

Charlie was in a headlock and Ethan hand a pistol to his head.

"Ethan DON'T" I begged.

"Never give up Alex" Charlie yelled as Ethan pulled the trigger.

In a puff of smoke Charlie fell to the ground, blood pooled around him as he reverted to his human form.

I stood there in shock, Charlie was gone, Ethan had just killed my best friend like it was nothing.

"You're turn" Ethan said as he raised his hand to shoot me.

Everything moved in slow motion, I used extreme speed and disarmed him, I threw the gun aside and backhand him with my paw spike. A massive gash adored his right cheek. I pinned him to the floor and summoned an aura sphere.

"Go ahead, do it" Ethan said.

I took a deep breath and dissolved the aura sphere. My bloodlust passed as quickly as it came.

"No, not even you, there's been enough killing today" I said sternly.

"Coward, you were always such a …" I cut Ethan off and kicked him in the head, knocking him out cold.

I turned to his team and said "here's your chance to do the right thing" I offered.

Sandman, Grinch and Truck threw down their rifles. Frost dropped his sniper rifle and spoke "we'll come quietly"

I then walked up to Charlie's body and closed his eyes. Just then my wrist com crackled to life.

"Cipher is retreating, Alex what's your status" Michael asked.

"Vault is secured, agent Daniels is" I couldn't say it.

"I'll send a medical team" Michael said,

"Don't bother, he's gone" I said in a hollow voice.

4 soldiers ran in and cuffed Ethan and his team.

"Take him to solitary" I said, pointing to Ethan.

"And those 4" a soldier asked.

"They surrendered peacefully, treat them with dignity" I ordered.

Then the medics arrived with a body bag, the look on their faces told me Charlie was far from the only fatality.

The put him in and began to carry him away. I stopped them and unzipped the bag around his head.

"Goodbye Charlie, you deserved better than this" I apologized solemnly.

With that they carried my friend away, another pointless casualty of war.

3rd person POV

Michael stood in the damaged control room while the 3 remaining shifters and Latios sat around a tabel. Multiple monitors were smashed with specks of blood all over the room. Michael's sleeves had been dyed red from helping a wounded agent

Cassie's eyes were red with tears, Jake was simply silent along with Connor.

"Today we lost a good Agent, and a good friend, Communications are down, along with the lustrous orb and half of our planes and vehicles. The purify chamber will take months to fix. We lost at least 150 agents, with many more wounded. I got nothing for you, if you want to leave, I won't hold it against you" he offered.

With that he sighed and left, leaving us alone.

* * *

Lana's POV

"Well done Victor" I said as he handed me the lustrous orb. He had retrieved it with a teleportation device while Ethan's team acted as a diversion.

"We got Sophia out, but Ethan and his team weren't so lucky" he grumbled.

"Unfortunate, but acceptable" I said as I put the orb in a specially designed briefcase.

"That should keep the energy stable while you take it to HQ" I said.

"I'll be sure to give the master a good report about you, the triton station seems to be in good hands" he complimented as he left.

I returned to my office and sat down. I had to admit the doctor's study was a nice space. I simply wished he wouldn't have secured his files so thoroughly. Only he knew the password to his computer. He never wrote it down in order to make himself irreplaceable.

Cipher's best hackers were trying to break through his firewalls but they weren't very optimistic.

My brother was a constant nuisance, if I saw him I wouldn't hesitate to end him. My powers were far beyond his, I was the most powerful member of cipher besides the master, and most of his power wasn't even his own.

Ardos's shift form was impressive, but his real strength came from elsewhere, and without that I could easily best him…

"Prefect Lana, may I come in" Kallahan asked over the intercom, snapping me from my thoughts.

"Enter" I responded.

Kallahan gingerly opened the door, he was holding a data pad.

"This is all we've been able to get off the doctor's laptop, my best technician says he found a gas to break the firewall" he said confidently.

"How so" I asked

"It's a virus he made that slowly eats away at a firewall than breaking through it, in 3 weeks we'll have everything" Kallahan explained.

"Very good, leave if you would" I requested.

Then I felt it, something was trying to read my mind, it had just formed a psychic link

"Lana, I sense where you are" my brother said.

"Oh really, good luck getting here" I tauntingly responded.

"Cipher put a lot of people in the ground today, I'm currently sitting amongst a pile of bags your friends filled" he scoffed.

"You didn't use our sibling link to make me feel bad, get to the point" I demanded.

"I'm coming for you, and when I find you, I'll kill you, I'll kill you dead" he threatened.

"We shall see brother dearest, we shall see" I said as I closed the link…

 **Author's note- another major death, I hope that people liked Charlie's last words, it was the best I could do…**

 **I even snuck in my favorite line from the 2nd best fighting game story mode ever , you'll get an imaginary thumbs up if you know what it is and where it's from.**

 **As for Ethan's team, with all the killing they've been doing before and after Altomare they simply decided enough was enough**.

 **Leave a review, I always appreciate it.**


	34. Chapter 34

Chapter 34

* * *

3rd person POV

"I have an idea" Alex announced as he entered the war room.

Everyone perked up, hoping for some good news. MRPA HQ was somewhat up and running after 2 weeks of repairs.

He sat down and laid out the plan, speaking slowly and clearly "We need to infiltrate a cargo ship and sneak on board one of their subs, then we find the location of their HQ, set charges and run the sub bay where a retrieval squad with sub pods will be waiting"

"That could work, but we can't predict the future, the cargo shipments are nearly impossible to track because they constantly rotate ships" Michael countered.

"Actually, I may have way to give us a edge" Connor said quietly.

"What" Michael asked before Connor shushed him.

"I have a friend in Itex forest who may give us some intel, but she is pretty untrusting of humans" Connor explained telepathically.

"Ok, go talk to her with Jake and Cassie" Michael said.

Connor nodded and motioned to Jake and Cassie.

As they walked out of HQ, Connor waved his hand in the air, the space around them began to ripple, like an isolated heat shadow.

"Teleport to Azelia town, I'll meet you there" Connor explained before dropping his illusions and flying away.

* * *

When the Simmons twins arrived in the forest Connor was waiting for them at the shrine in the center of a ring of trees.

"My friend is a little...eccentric, but she may have the intel we need. Just don't get flustered by some of her remarks" Connor said vaguely.

"Hehehe, oh Connor, you know me so well" a high pitched female voice said from every direction.

There was a flash of light and a small green Pokémon with round toeless feet, three-fingered hands, and clear wings on its back appreared. It had a round head that came to a curved point. Its large innocent baby-blue eyes were outlined with thick black rings, and a pair of green antennae with blue tips adorned its forehead.

"Connor, you've come back to see ME!" Celebi said doing a loop in the air.

"Yea, we need your help" Connor asked politely.

"Oh, you need advice about your son, he's got a bright future don't worry" she said casually.

Connor's eyed went wide as dinner plates, Celebi had just spilled his greatest secret to Jake and Cassie.

"You have a SON!" Jake asked flabbergasted.

"I wanted to keep it a secret Celebi, for his own safety" Connor said through clenched fangs.

"Sorry, how can I make it up to you" she asked, she looked like she was about to cry.

"It's ok, just tell us when Cipher is making a shipment to their underwater factory and we'll call it even" Connor sighed.

"Ooo, that's tough, I'm not really supposed to tell someone the future" she said looking away.

"Please, no one is safe if Cipher wins" Cassie begged.

"Oh fine" Celebi said in a mischievous tone.

Celebi closed her eyes, she was silent for a while before she opened her eyes and spoke in a serious voice.

"3 weeks from now Tuesday morning" she whispered in Connor ear.

"Thank you" Connor responded quickly.

"Your welcome, now you might wanna leave " Celebi said quickly.

"Why?" Connor asked.

"Oh Cipher is about 3 miles away, the master is personally overseeing my capture" she casually explained.

"WHAT" Cassie, Jake and Connor said in unison.

"We'll help you fight" Jake said with a fire in his eyes.

"She'll be fine, let's go" Connor ordered.

"But…" Cassie began.

"No buts, teleport NOW" Connor yelled.

Cassie and Jake disappeared into a ball of fire and electricity respectively.

Connor tucked his wings in , he looked back at Celebi and said "take care of yourself" before going invisible and flying away.

Celebi was about to teleport but a tranquilizer dart streaked past her. Soldiers with shadow Mightyanas emerged from the trees.

"Fire at will" one ordered.

Celebi smirked, her eyes glowing green.

The air seemed to ripple, the darts froze midair along with everything in a 20 feet radius. Celebi had stopped time completely.

She focused on the rifles and began to fast forward time, patches of rust appeared and eventually the rifles turned to dust.

Celebi did the same to the darts and allowed time to resume normally.

"What just happened" the soldiers asked in disbelief.

Celebi laughed, but a shadow ball hit her out of nowhere and she was knocked against the shrine, landing on the ground.

Celebi tried to get airborne but another shadow ball hit her.

"I'm afraid you won't be getting away from us" Ardos said as he walked out of the shadows.

"Oh my dear Ardos, I can't be caught" Celebi laughed despite her injuries.

"It would not seem that way" he scoffed.

"You just can't see it, but I can" Celebi vaguely threatened.

"Oh please enlighten me, what do you see that I cannot" he taunted.

"I see your death, your blood will be your undoing" Celebi said before a green flash blinded Ardos's vision.

When Ardos could see again Celebi was gone, a high pitched laugh echoing throughout the forest.

"Nonsense" Ardos muttered.

The commander walked up to the master. He was stoic and emotionless, but if one looked closely through his glasses his eyes betrayed his facade.

For the first time in years, the master was unsettled….

 **Author's note- well, that's not ominous or foreboding at all.**

 **yes this chapter is a little shorter but i decided that was the natural best part to end the chapter.**

 **leave a review and tell me what you think :)**


	35. Chapter 35

Chapter 34

* * *

3rd person POV

Within MPRA HQ the entire agency was planning the attack on the triton station, the plan to do so however was pretty unfinished.

"It's time I come clean" Connor conceded.

"What do you mean"? Michael asked.

"I've been informed that cipher's next shipment is arriving in one week, and thanks to my sibling link, I managed to find out something far more important" he said

"Whoa, hold on, you have a psychic link to your sister!" Cassie exclaimed.

"She' been shutting me out but I managed to sneak in and learn some new things" Connor said defensively.

"Spit it out Connor" Alex demanded.

"Every remaining admin is meeting at the triton station, and the master is personally overseeing the conference, leaving their HQ in turnback cave under guarded" he explained.

The entire room went quiet, everyone looked at Connor like he had two heads. Cipher was about to have all its leadership in one place and they knew when and where.

"Well, do you have a plan?" Michael asked.

"It's not the best but I'll tell you" Connor said as he pulled up a readout of the station.

"We can't sink it, they have defenses for depth charges and torpedoes, But I may have an alternative" he alluded, pointing at the support columns underneath the facility.

"If we can keep the master occupied, I'll take care of Lana. Then I'll blow the supports. We'll launch a missile barrage at turnback cave and collapse the cave to stop reinforcements" Connor explained, a hint of hesitation was in his voice at the mention of his sister.

"Not a bad idea, but how do we keep Ardos busy?" Michael asked.

"Me, Cassie, Jake and Dana can do that, we just need to get inside the facility" Alex suggested.

"I got it!" Connor exclaimed.

"What do you have in mind?" Jake asked.

"I can use my illusions to get us near the sub with scuba gear, then we latch onto it with a magnetic clamp and ride it to the base, you four will sneak inside and distract the admins while I set the charges. Then I'll, deal with my sister to cover your escape" he said, the hesitation even more apparent.

"I have one problem with this" Michael interrupted.

"What's that?" Jake asked.

"It's you five against an army, we need a better plan, we may have to wait, and I'm against just destroying everything we may be able to salvage some equipment " he said scratching his chin.

"No, were not passing up this opportunity, and you are not saving ANY of Cipher's tech. You can support us any way you want, but we have to strike now" Connor said firmly.

Michael pointed his finger at Connor,his face showing rage. However, it passed as quickly as it came, he slumped down in his chair and shook his head.

"This is the right play, you have to trust me" Connor begged.

Michael averted his eyes, clearly mulling over every available opinion.

"Well, I guess your calling the shots now, whatever you decide to do, I'll support you" he said in a tired voice.

"Thank you" Connor whispered.

Connor turned to crowd of agents "Alright, we have one week, I want every agent with scuba training to help those without it, gear up and get every chopper we have airworthy" he ordered

Everyone looked at Michael, he scoffed and said "what are you looking at me for, get moving"

The crowd of agents dispersed, heading in different directions to inform the rest of the base and begin preparations

Connor walked away, heading to the hanger. Jake took notice and ran after him.

* * *

Jake's POV

I ran up to the catwalk above the main hanger. Connor was overlooking the scene below. The entirety of the MRPA's forces were preparing for the attack.

"What's bothering you" I asked.

"I'm fine, it's just nerves" he said dismissively.

"Your a terrible liar when your troubled, so spit it out" I asked sternly.

He shook his head and muttered "Im fine, we need to focus on the task at hand" trying to change the subject.

"Cut the tauros crap, what is bothering you, we need to talk it out so your 100 percent in the game" I demanded.

He closed his eyes, took a deep breath and looked away, clearly avoiding eye contact. After a long pause he spoke.

"I need to put my sister down, but I don't know if I have the strength to go through with it" he admitted

"She's a murdering psychopath,that's not someone you save, that's someone you stop" I reminded him.

"I know, but she was a good person and a great big sister, those memories are the hard part" he explained, clearly reminiscing about her.

I looked at him for a long time, he was deep in contemplation, he was fighting himself to make a decision.

"One way or another, my sister and I are ending this, if I don't make it…" he began only for me to interrupt.

"Don't do that, don't think about that possibility" I told him firmly.

His illusion shattered, he wasn't concentrating enough to keep it up. The green Latios that had never shown fear had a single tear rolling down its face.

"If I don't make it, go to the sevii islands. Tell Lisa and Zander that I love them and that I died doing what I thought was right" he requested.

I was taken aback, but nodded solemnly.

He let a small smile escape his mouth, then reapplied his illusion and left.

In 3 days, the war would end, for better or worse….

 **Author's Note**

 **yes, there are only 3 chapters left then the epilouge, the hiatus was due to the fact that i had to decide the future of this story, rest assured it will be a fitting finale...**

 **leave a review :)**


	36. Chapter 36

Chapter 35

* * *

3rd person POV

"Viper-24 your cleared for departure" The traffic controller announced.

With a roar the VTOL shot up into the clouds.

Connor stood up as Jake, Cassie, Alex and Dana were putting on their scuba gear.

"You all know what to do, but keep in mind that we have plan B and the Checkmate as a last resort" Connor reminded them.

Alex winced at the mention of checkmate, if everything went south Connor would send a psychic message to Michael. The MRPA would launch every missile in their arsenal, hopefully destroying the triton station and turnback cave in one fell swoop.

Michael recommended to capture the admins and the master for interrogation, that way they could tie up every loose end. Connor was opposed to this, but Michael remained him that every Cipher agent deserved a fair trial under international law. Connor begrudgingly agreed but said he wouldn't hesitate to end the master and his sister. They could only be taken alive if they were safe to transport.

Once everyone was suited up they headed to the back of the VTOL where another shiny new toy was waiting.

The DTV-29 looked like a jetski mixed with a torpedo. It was still experimental but these 4 units were deemed mission ready. They could move up to 58 miles per hour and were invisible to sonar.

"This is as far as I can take you without being detected, good luck guys" the pilot said as the VTOL came to a hover above the water.

Everyone mounted up save for Connor, who dropped his illusion and put on a special made MRPA rebreather. The green Latios dived into the crystal clear alolan water.

Alex gave Cassie a wink and the four shifters leaned forward. The DTVs lurched and began to slide down the ramp. They were airborne for a fraction of the second then the world went silent.

"Alright, let's get moving" Connor ordered via telepathy.

The team glided through the water, carefully avoiding sea life as they went along. However as they were nearing the rendez-vous point something appeared on sonar. It was massive, as large as Wailord and moving as fast as a speedboat.

"It's the sub!" Alex said nervously.

"No it's not, it's too early and way too big" Cassie dismissed.

Connor's eyes went as wide as dinner plates, all he could say was "Oh no"

A swarm of water pokemon went past, they were clearly swimming away from something. Out of the depths emerged a leviathan unlike anything they had ever seen. The Pokémon's two massive pectoral fins each had four white square-shaped nails. Its deep blue body and white chin had two small spikes protruding under it. Above each eye are two white, oval-shaped spots. It had red stripes around its chin, eyes, dorsal fins, and torso. These stripes were glowing red. Its tail was tattered with four trailing parts, the inner ones being smaller than the outer. Its eyes were small, yellow, and shadowed with black.

"BEGONE HUMANS, YOU TRESPASS IN MY OCEANS TO PLUNDER ITS RESOURCES FOR THE LAST TIME" a voice boomed telepathically.

"We're not here to steal" Cassie responded.

The beast paused and asked "how can you respond human"

"I'm more than meets the eye, we don't want to fight, we want to go to the triton station and destroy it" Cassie explained slowly.

"The human building nearby?" the beast questioned.

"Yes" Cassie responded.

The beast stared down the group, but then took notice of Connor coming forward

"Lord Kyogre, I am Connor, soul survivor of the Sinnoh Lati herd and Son of Jebediah, we have come to stop the group known as Cipher who is polluting your seas, they plan to open a gateway to the distortion world and unleash Giratina" Connor explained in a formal tone, revealing a glowing blue brand on his arm. It looked like two crescent blades with an eye in the center.

Kyogre's eyes relaxed instantly, he looked at Connor intently for a moment then spoke.

"You look so much like your father, I owe him a great debt, proceed" Kyogre said before turning around and swimming back into the abyss beneath them.

"What was that" Alex said, still dumbstruck.

"Kyogre, the creator of the oceans and one of the most powerful beings in the world " Connor responded.

"But what about this Giratina" Jake asked.

Connor paused at that question, this was going to be a difficult thing to explain.

He took a deep breath from his rebreather and said "Giratina, is part of the triangle that makes up existence itself. Time, Space and Antimatter. Three beings control this triangle under the guidance of the original one. Giratina in particular controls antimatter and was banished to a realm on the opposite side of ours, a place one might call the distortion world."

"So, let me get this straight, Cipher is going to unleash an ancient being who controls Antimatter itself" Jake questioned, barley believing what he had just said.

"Yup" Connor said nonchalantly.

The submarine appeared on the scopes, it was almost here. Connor looked at the team and said "power down, let it pass"

The team powered down the DTVs. They simply sat there until the sub was right above them. Everyone activated their magnetic gloves and grabbed the outside of the sub.

"Alright, hang on tight, once their docked we make our move…."

* * *

Lana's POV

"Right this way master" I offered as he disembarked.

"I assume the other admins have arrived on schedule?" He asked as his Bisharps came to his side. The two blue Bisharps were closest with 4 red ones behind them.

I nodded as we entered the hallway leading to the throne room.

The entire staff of the triton station was present, all standing at attention as the master walked by.

"The gateway is charging as well?" He inquired.

"Yes master, we managed to reproduce Gregavich's design and began powering up around an hour ago, all the admins are waiting on the throne room, the device is there as well" I explained.

His lip curled into a smile, a rare sight on the master's usually blank face.

"Well done Lana, I never could have done this without you, your loyalty will soon be rewarded" he said via telepathy.

I smiled and opened the massive steel doors via telekinesis. Victor, Sophia and Nikolai were sitting at a tabel with the throne at the head.

Ardos looked puzzled, but he sat down and allowed me to join him.

"Where is the gateway" he asked sternly.

I smiled and pointed to a wall, "its behind that wall, a lead lined chamber to keep the MRPA from tracing the energy signature"

"Open it, the MRPA will never be able to get here in time, once the gateway opens we will be unstoppable"

I hesitated for a moment, but pressed the button. The device was self sustaining now, even if the entire station lost power the shadow energy it was creating would power it for days.

The wall slid away revealing a giant metal ring with a surging ball of black energy in the center. The facility A.I spoke clearly saying "gateway at 45%, 90 minutes remaining"

Ardos raised his arms above his head, "at last, the day has arrived, the world will be ours" he announced triumphantly.

"Warning, intruders detected in sub bay two" the computer blared.

Ardos shook his head "no no no not now" he muttered under his breath.

The admins stood up and turned to Ardos, awaiting orders.

"GO, BUY ME TIME, SEAL SECURITY DOORS AND ACTIVATE ALL DEFENSES" he yelled at the top of his lungs.

The entire room descended into chaos as the admins and soldiers ran out of the throne room.

"Lana, wait outside, you are the last line of defense, understand?"

I nodded rapidly and ran out as well. If the MRPA wanted a fight we would oblige them….


	37. Chapter 37

Chapter 37

* * *

Dana's POV

"Go go go" Alex yelled as he bone rushed a soldier in the face.

We ran as fast as our shift forms could move. we came to the hub of the facility with three massive doors on each side.

"Which one?" Cassie asked.

Alex frowned and kneeled, placing his paw on the floor and closing his eyes. His four aura sensing organs on his head rose up.

After a moment he stood up and pointed to the door directly ahead.

"You're sure?" Jake asked.

Alex nodded and ran towards the door. He pressed his paw against it and felt it up.

"It's reinforced titanium, we can't get through this" Alex admitted.

Before anyone could respond all three doors opened, over 100 soldiers came in from all sides.

"Your surrounded, give up!" the commander yelled.

Cassie smiled and said "yea no"

"Dana shield now!" She warned telepathically.

I tackled Alex and erected a psychic barrier while Jake used protect. With a roar Cassie unleashed a giant blast of electricity that engulfed the entire room. The Raikou stood triumphantly as every soldier fell to the ground twitching.

As I dropped my shield I noticed a lone figure standing at the door, it was a machamp cracking his knuckles.

"Impressive,SEAL THE DOORS" he yelled.

I ran as fast as I could but the door was faster. Only Jake, Cassie and Alex made it through.

"All alone little lady" the Machamp taunted.

"I'm more than enough to take you on" I yelled.

* * *

3rd person POV

"We lost Dana" Cassie shouted.

"No time, keep moving" Connor ordered mentally.

"How's the charges coming?" Cassie asked as she thunderbolted a squad of soldiers.

"Three more then I'll meet up" Connor esponded.

A massive jet of fire came straight at Cassie, only for Jake to jump in front and take the flamethrower head on.

The raging inferno parted around her then vanished. Steam was wisping around Jake's shaggy brown fur but he was unharmed from absorbing the energy.

A silver ninetails hissed from across the room. "Damit, I hate flash fire, you delinquents really think you even have the slightest chance of winning against us?"

Alex sighed "yeah shut up"

He shot an aura sphere and sent Sophia flying. She hit the wall, falling to the floor unconscious.

Another man in armor walked out of the shadows wielding a sword. Only to be knocked out by an invisible object.

Connor materialized in front of us, the team ran down the hall only to come to a final massive door. In front of which stood an all too familiar figure.

"It's been awhile" Lana stated in a neutral voice.

"Not long enough" Cassie replied.

Cassie and Jake tensed their muscles, ready to fight. Connor shook his head and hit Lana with a luster plurge. The beam pinned her to the wall.

"This is my fight, stop the master" Connor ordered as he held out his claw in the direction of the door.

The door began to glow, it became see through like a piece of glass.

"Go NOW" he yelled before throwing Cassie, Alex and Jake through the door with telekinesis.

The door returned to normal, leaving the two Lati alone in the room

"Finally come to face me? Or are you gonna freeze up" Lana taunted as she dropped her human guise.

"I'm not running, not again, my friends are depending on me" Connor stated, his voice sounded like he was reassuring someone.

"Don't be ridiculous, you can't beat me" Lana said with a tone of finality.

Connor then took notice of a bluish stone in a collar around Lana's neck. He scowled as soon as the realization dawned on him.

"You have the audacity to wear that, that family heirloom that you stole off of Mom's corpse, have you no shame!" He asked.

"Its rightfully mine, and you have its twin" she jeered .

"ENOUGH! Your selfishness and lust for power have consumed you, you are a disgrace to your bloodline" Connor reprimanded.

"Don't lecture me, I see through the lies you spew, humans are repulsive beasts who exterminate or exploit those higher than them. Giratina will bring justice to this world and put humanity in its rightful place" she proclaimed.

"Lana, are you even listening to yourself? The world Giratina will create will only be prosperous for one person, him! It's not a paradise, it's damnation" Connor explained.

Lana shook her head and said "Hush, it is a world you shall soon see, and my lord himself shall witness your fall"

"Your a psychotic monster, as far as i'm concerned my sister died a long time ago, Im ending this here and now" Connor conceded

"So that is how it's going to be?" Lana asked.

"That is how it has to be" Connor responded coldly, a single tear escaping his eye.

The two lati charged at each other, moving faster than the eye could see. Connor rammed Lana as both of them went intangible and flew through the wall of the facility.

Their story would end here...

* * *

Dana's POV

"That all you got" the Machamp taunted as he hit me with a poison jab.

I staggered backward from the blow, this Machamp was clearly tougher than me.

I mega evolved and focused on the ghostly arms on my back, sending them to attack him. My mega form's greatest advantage was these nearly invisible arms.

He was punched right in the jaw, knocking the saliva out of his mouth. I picked him up with psychic and threw him up to the ceiling. He fell straight down like a rock.

Before he could get up i used my arms and hit him over and over while he was down. He shakily stood up, sucking air as he got to his feet.

"You little bitch" he muttered as he ran towards me, readying a dynamicpunch.

I sidestepped at the last second and hit him with zen headbutt. He fell to the ground, reverting to his human form. It was over, I had defeated the Cipher admin. Now i needed to help my friends...


	38. Chapter 38

Chapter 38

* * *

3rd person POV

High above the Triton station two figures shot out of the water. One shot a luster plurge as the other shot a mist ball. The two attacks collided, creating an explosion the size of a ocean liner.

As the smoke cleared a red blur charged at the green Latios, moving several times the speed of sound. The two Lati clashed, creating shockwaves as they fought.

Lana mega evolved and fired another mist ball, but Connor simply went intangible and the attack passed through him. She growled and resumed her charging. The two legendaries ramed each other over and over. The fight was happening so fast that all one could see was two flashes of light and the shockwaves from the collisions.

For now, the battle was at a standstill.

* * *

Alex's POV

When we entered the room we were greeted by 8 Bisharps standing at the ready. 2 of which were blue instead of red.

"KILL THEM" a voice shouted from across the room.

The Bisharps ran at us, only to be hit with a tidal wave of fire from Jake. All 8 fell to the ground, smoking and tinged black.

We all walked past them and came face to face with a device unlike anything we'd ever seen. It was a massive metal ring, with a black ball of energy in the center. It was pulsing like a heart, it looked like it was made of black sludge. At the base was a spiderweb of hoses and circuitry.

Next to the device at a computer terminal was a man clocked in a blue and grey robe. His hands were obscured by his long sleeves. The long hair on his head was deep blue, with just the slightest hints of grey around the edges. A stone cold face with black sunglasses covering his eyes gave off a vibe of pure intimidation.

He looked at us in silence for a moment, clearly sizing us up. Then he spoke. "The three I've heard so much about, I'd imagined you'd be a little older"

We all stood their confused, taken aback by his casual demeanor.

"I am Ardos, grandmaster of Cipher and son of Greevil, the founder of Cipher. I must say that I never expected my own nephew to be one of the biggest thorns in my side" he confessed, looking directly at me.

"What, you're saying that I'm, no that's not possible, my uncle died in a..." I denied before he finished my sentence.

"Car crash, that's what Eldes told you, the coward, too ashamed of his family to tell the whole truth" he muttered.

I stood their in shock, his aura was similar to my father's after all.

I assume you're Latios friend is fighting Lana?" He questioned.

I nodded, my head still spinning from this revelation.

"I see, a pity she won't be here to see the work completed" he said, genuine sadness apparent in his voice.

"You aren't finishing anything" Jake snarled as he and Cassie fired a thunder and fire blast respectively. The portal simply absorbed the attacks midair.

"I'm afraid that won't work, that's pure shadow energy, not the diluted form we use to make shadow Pokémon" he explained.

"We've come too far to give up" I stated firmly.

"A shame, farewell nephew" he sighed before unleashing a wave of shadow energy from his body. It took the form of a black fog blowing towards us like wind. I stood tall as it blew us back. I felt horrible, as if me entire body was on fire. A feeling of hopelessness and dread consumed my mind. I looked beside me, Cassie and Jake were unconscious on the ground.

"Impressive, but futile" he taunted as the winds intensified.

I fell to my knees, my will was the shadowy wind pummeled me.

"Feel the despair, feel your very live force being drained away" Ardos said maliciously.

"I WON'T GIVE UP" I yelled. As I said this my body began to glow, my aura surged from within me as I mega evolved out of instinct.

I got to my feet, I could feel my power skyrocketing. That deeper well of aura within me was finally unleashed. A pillar of blue light formed around me, dispelling the wind.

Ardos stepped back, clearly surprised. For all his power he was legitimately worried.

He regained his composure and shifted. He fell on all fours as scales grew over his skin. Massive blade like wings formed on his back as his body grew. A black salamence with a mega stone around his neck was soon before me.

"An admirable effort, but all in vain. The gateway will be open in mere minutes. Whether I win or lose this fight you've already lost" he boasted.

"Not yet, we fight until the end" I yelled.

In response he mega evolved, after a brief flash of light his wings melded together into a single huge, crescent-shaped wing, the hard, yet very flexible properties of the wings allowed them to be used as a blade. His face, neck, body and tail became narrower, and his tail was noticeably shorter in length. The ridges above his eyes were now far less prominent, and he no longer possessed the thick, gray scaling over his lower jaw. Instead, the smooth red flesh underneath has been left exposed, increasing the streamlined appearance.

I fired an aura sphere, he took it head on and was unfazed.

He flew at me, his crescent wing ready to cut me in half, I rolled to side just in time. He was so faster that even my mega form was struggling to keep up.

"Time to die" he yelled as he changed up a dragon pulse.

"I cannot lose" I yelled.

I summoned every ounce of aura I could, he unleashed a shadow infused dragon pulse as I fired a massive beam of aura.

The beams were at a standstill, i focused as hard as I could, trying to keep up.

Suddenly my beam pulled ahead and sent his attack back at him. He was shoved into the portal as both my aura and his shadow energy exploded in unison.

I looked up as the smoke cleared, the device was destroyed.

Ardos reverted to his human form as the black ball of energy levitated towards him. Two glowing red orbs formed within the abyss.

"You have failed me" a serpentine voice said.

"My lord please I can make this right" Ardos begged.

"Our deal issss forfeit, I will be taking my power back now" the voice said.

"No please" he screamed.

A black smoke began to pour out of his body. As this happened wrinkles formed all over his skin. His hair turning silvery white. The last of the black smoke left his body as Ardos let out one last feeble cry. His body dissolved into a pile of ashes.

The orb then began to shrink, then it vanished from existence.

I didn't have time to comprehend what I had just witnessed, my aura faded and I blacked out.

* * *

Connor's POV

"Lana, give up" I yelled as she panted, clearly exhausted.

"N-never" she jeered, her voice was horse as she sucked air.

"Don't make me do this" I begged.

"You're gonna have to kill me" she yelled.

She charged at me one final time, I dodged effortlessly. My claw went intangible, all I could think was one phrase.

I stabbed her straight in the heart, she wasn't nearly fast enough to stop me. As she coughed up blood I whispered in her ear "I love you, and I'm sorry" with that I removed my claw and she fell, her mega form disappearing as she hit the water. I used our sibling link to confirm. As I tried to reach out the link was cut, something only death could achieve.

I couldn't hold the tears, for the first time in years, I wept.

A voice entered my mind "Connor, Ardos is dead, we're clear of the station with Alex, Cassie and Dana, we disabled the other subs,are the charges set?"Jake asked.

"Do it" I ordered, failing to suppress a sob.

A geyser of water erupted from the ocean, then the ocean calmed.

I sighed, all I could say was "it's over"...

 **Author's note- thanks for all the support over the course of this story, there's a short epilogue but other than that this is the end of this story.**

 **Tell me what you think of the finale**


	39. Epilogue

Epilogue

* * *

3rd person POV

Somewhere beyond space and time a shadowy figure roared at the sight in front of it. A window to earth showed a massive explosion under the sea. Decades of planning and manipulating mortals had been for naught once again.

The beast closed the window , and flew towards one of the infinite floating islands hovering above the abyss. The islands were cold and lifeless. Time didn't flow, and Space itself was unstable. Islands faded in and out of existence as the serpentine figure passed by.

Soon it came to it its destination and focused its power on a crystal in the center of the island. A man in a lab uniform with a golden G on the breast pocket fell to the ground as the crystal dissolved.

I grant you a reprieve, I will use my remaining power to send you to earth, with Cipher destroyed only a small group of my followers who have remained separate and hidden for centuries remain. Lead them and prepare an army for my arrival.

"Yes my lord" the man said as he straightened his light blue hair.

"Be warned, your time here has stopped your aging but it will be decades before I have enough strength to speak with you again. Once I have absorbed enough power I will punch open a hole to earth where the barrier is weakest"

"I understand" he replied slowly.

With that the creature's eyes glowed and a small portal opened. The man bowed as the beast pumped the last of its power into the portal.

"Go my disciple, prepare my way Cyrus" it ordered.

"Yes lord Giratina" Cyrus said before diving into the portal…

* * *

20 years later…

"Alright, Kelly, Charlie dinner time" Cassie called to her two children. Her daughter and son ran in as Alex pulled the pizza out of the oven.

"Daddy, I used thundershock" Charlie exclaimed.

"Really, great" Alex praised.

With that the family ate supper, after the kid were in bed Cassie heard a knock at the door.

Cassie opened the door and gasped as Alex came up behind her .

"Connor?" Cassie asked.

Connor, in his usual human guise smiled.

"How are you?" He asked as he sat down on the couch

"I've been great, just looking for a job still" Cassie said as Alex handed Connor a cup of tea.

"Well that's actually why I'm visiting" Connor admitted.

Cassie looked confused.

I've already opened up one school in Kalos, Dana is doing well as headmistress. With my school for shifters in Sinnoh already 3 years old, I was wondering if you would oversee the constitution of a school right here in Olivine city" he offered.

"I'll do it" Cassie agreed.

"Wait Cassie don't be so hasty" Alex interjected.

"No Alex, I want to help people like us" Cassie stated firmly.

Alex backed off.

Cassie smiled as the thoughts of her new position filled her mind. A new role for her to play helping people was exactly what she wanted.

The future was bright…

 **Author's note- thanks for all the support over the course of the story, you guys really keep me inspired.**

 **special thanks**

 **Ol' 3lue Eye For beta reading the first half of the story and supporting me throughout the course of my writing.**

 **storylover Vodhr for giving me advice and allowing me to use his ideas involving the lati.**


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